=============================================================================== 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/rebuilderdxJKJah/inputs/iqtree3_3.1.1+dfsg-1_amd64.buildinfo Source: iqtree3 Version: 3.1.1+dfsg-1 rebuilderd-worker node: osuosl44-amd64 +------------------------------------------------------------------------------+ | Downloading sources Mon, 20 Apr 2026 19:41:15 +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 [148 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/main Sources [10.5 MB] Get:10 https://deb.debian.org/debian trixie/non-free-firmware Sources [6,552 B] Get:11 https://deb.debian.org/debian-security trixie-security/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 [99.3 kB] Get:15 https://deb.debian.org/debian trixie-backports/main Sources [192 kB] Get:16 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [2,984 B] 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 [10.6 kB] Get:20 https://deb.debian.org/debian sid/main Sources [11.5 MB] Get:21 https://deb.debian.org/debian experimental/main Sources [435 kB] Get:22 https://deb.debian.org/debian experimental/non-free-firmware Sources [2,568 B] Fetched 34.4 MB in 4s (9,466 kB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/i/iqtree3/iqtree3_3.1.1%2bdfsg-1.dsc' iqtree3_3.1.1+dfsg-1.dsc 2213 SHA256:54602b6f93eb9a320376ad3933acdb2886fd85590ea0393472c7376c37ec6031 'https://deb.debian.org/debian/pool/main/i/iqtree3/iqtree3_3.1.1%2bdfsg.orig.tar.xz' iqtree3_3.1.1+dfsg.orig.tar.xz 2314716 SHA256:abafa0ab7d5b33a214831dbb7e5e7c80b67572b57787f34b961617d4e79d30f3 'https://deb.debian.org/debian/pool/main/i/iqtree3/iqtree3_3.1.1%2bdfsg-1.debian.tar.xz' iqtree3_3.1.1+dfsg-1.debian.tar.xz 23900 SHA256:033c60708e37fa4c575779fa2b2a2f03320f62c7a13fda2f4702769b75cd7c6b abafa0ab7d5b33a214831dbb7e5e7c80b67572b57787f34b961617d4e79d30f3 iqtree3_3.1.1+dfsg.orig.tar.xz 033c60708e37fa4c575779fa2b2a2f03320f62c7a13fda2f4702769b75cd7c6b iqtree3_3.1.1+dfsg-1.debian.tar.xz 54602b6f93eb9a320376ad3933acdb2886fd85590ea0393472c7376c37ec6031 iqtree3_3.1.1+dfsg-1.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Mon, 20 Apr 2026 19:41:20 +0000 | +------------------------------------------------------------------------------+ + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdxJKJah/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdxJKJah/inputs/iqtree3_3.1.1+dfsg-1_amd64.buildinfo Rebuilding iqtree3=3.1.1+dfsg-1 in /srv/rebuilderd/tmp/rebuilderdxJKJah/inputs now. /srv/rebuilderd/tmp/rebuilderdxJKJah/inputs/iqtree3_3.1.1+dfsg-1_amd64.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/iqtree3-3.1.1+dfsg I: verifying dsc... successful! Get:1 http://deb.debian.org/debian unstable InRelease [187 kB] Get:2 http://snapshot.debian.org/archive/debian/20260418T022809Z 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/20260418T022809Z unstable/main amd64 Packages [10.4 MB] Fetched 21.1 MB in 2s (10.0 MB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20260418T022809Z/dists/unstable/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted 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/tmpir8ubq_o/libmpc3_1.3.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 16-20260322-1 [886 kB] Fetched 886 kB in 0s (70.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv0rgop3s/libgfortran5_16-20260322-1_amd64.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 (17.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa62i_2w5/libpam-modules_1.7.0-5+b1_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 (8761 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpote7eia2/debianutils_5.23.2_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 (84.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplet9a7va/dpkg-dev_1.23.7_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcrypt1 amd64 1:4.5.1-1+b1 [96.4 kB] Fetched 96.4 kB in 0s (0 B/s) dpkg-name: info: moved 'libcrypt1_1%3a4.5.1-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp11mn8xx6/libcrypt1_4.5.1-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libasan8 amd64 16-20260322-1 [2889 kB] Fetched 2889 kB in 0s (115 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6ioac7la/libasan8_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libseccomp2 amd64 2.6.0-2+b1 [52.2 kB] Fetched 52.2 kB in 0s (4644 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmcwzjgi8/libseccomp2_2.6.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z unstable/main amd64 libblkid1 amd64 2.42-3 [172 kB] Fetched 172 kB in 0s (14.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4bwar3lx/libblkid1_2.42-3_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/tmpw936i0cn/libgssapi-krb5-2_1.22.1-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libncl-dev amd64 2.1.21+git20210811.b1213a7-6+b1 [600 kB] Fetched 600 kB in 0s (16.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprr_53c_y/libncl-dev_2.1.21+git20210811.b1213a7-6+b1_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 (5099 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfnyuqnsh/libgdbm-compat4t64_1.26-1+b1_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/tmpyvpp4_90/pkgconf-bin_2.5.1-4_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/tmpht3vs5vb/g++-x86-64-linux-gnu_15.2.0-5_amd64.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/tmpw1s5db0k/libatomic1_16-20260322-1_amd64.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/tmp6agrdzcw/libxxhash0_0.8.3-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z unstable/main amd64 libmount1 amd64 2.42-3 [212 kB] Fetched 212 kB in 0s (19.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbd4mau9b/libmount1_2.42-3_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 (386 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr4s0o061/time_1.9-0.4_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/tmps78s6kqz/cpp-15_15.2.0-16_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.20.0~rc2-1 [408 kB] Fetched 408 kB in 0s (35.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpat5frt5_/libcurl4t64_8.20.0~rc2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libamd-comgr3 amd64 7.0.2+dfsg-3 [13.9 MB] Fetched 13.9 MB in 0s (181 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9lfk4qm5/libamd-comgr3_7.0.2+dfsg-3_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 (26.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp18zw05ld/liblzma5_5.8.3-1_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 (33.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpniws4y76/libtinfo6_6.6+20251231-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libacl1 amd64 2.3.2-3 [32.7 kB] Fetched 32.7 kB in 0s (2563 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9t3tlfs3/libacl1_2.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-6 [494 kB] Fetched 494 kB in 0s (43.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz_1tlxsk/autoconf_2.72-6_all.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 (55.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1340hi7g/xz-utils_5.8.3-1_amd64.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 (1951 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbrvm5rib/libnuma1_2.0.19-1+b1_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/tmpuk50a3l4/libevent-extra-2.1-7t64_2.1.12-stable-10+b2_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/tmp46_q_9cz/libnghttp3-9_1.15.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgprofng0 amd64 2.46-3 [820 kB] Fetched 820 kB in 0s (62.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv7m9xc0l/libgprofng0_2.46-3_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 (755 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxsf4xbow/liblocale-gettext-perl_1.07-8_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 (5238 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpelrzr0uo/libyaml-cpp0.8_0.8.0+dfsg-9_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/tmp90_vzrk6/cpp_15.2.0-5_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 (103 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbb4vx4ig/gettext_0.23.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.90.0.2 [3064 B] Fetched 3064 B in 0s (218 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpez18orkx/libboost-dev_1.90.0.2_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/tmpjg8aae8d/libidn2-0_2.3.8-4+b1_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 (3408 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9lbfiopc/gcc-15-base_15.2.0-16_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z unstable/main amd64 libc-dev-bin amd64 2.42-14 [37.5 kB] Fetched 37.5 kB in 0s (3566 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpksisxqxq/libc-dev-bin_2.42-14_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 (59.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph_vwc1bb/libstdc++6_16-20260322-1_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/tmpzk56n8d4/libjsoncpp26_1.9.6-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b3 [14.1 kB] Fetched 14.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxzl027no/libxnvctrl0_535.171.04-1+b3_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 (119 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuo21dvdk/binutils-common_2.46-3_amd64.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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp67tnrd1v/libibumad3_61.0-2_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/tmpvh4dsnpp/libjansson4_2.14-2+b4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z unstable/main amd64 libsmartcols1 amd64 2.42-3 [144 kB] Fetched 144 kB in 0s (12.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzuq581e0/libsmartcols1_2.42-3_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 (28.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpugeony4s/libevent-dev_2.1.12-stable-10+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z unstable/main amd64 linux-libc-dev all 6.19.12-1 [1978 kB] Fetched 1978 kB in 0s (96.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0gqhq2u0/linux-libc-dev_6.19.12-1_all.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/tmp6caamf3e/libuchardet0_0.0.8-2+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 (151 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphfr9og6j/libz3-4_4.13.3-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtsan2 amd64 16-20260322-1 [2573 kB] Fetched 2573 kB in 0s (60.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpje8u2oqk/libtsan2_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbinutils amd64 2.46-3 [548 kB] Fetched 548 kB in 0s (44.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcb037mwl/libbinutils_2.46-3_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 (27.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpog5jtfhg/ncurses-base_6.6+20251231-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Fetched 319 kB in 0s (31.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9wbvx8e3/libjs-jquery_3.7.1+dfsg+~3.5.33-1_all.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 (11.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaxkbcgp5/libuv1t64_1.51.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsepol2 amd64 3.10-1 [307 kB] Fetched 307 kB in 0s (30.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdtcex2fi/libsepol2_3.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.10-1 [154 kB] Fetched 154 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpudicqmrv/openmpi-bin_5.0.10-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z unstable/main amd64 bsdextrautils amd64 2.42-3 [99.4 kB] Fetched 99.4 kB in 0s (7879 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1ek707cn/bsdextrautils_2.42-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.31 [932 kB] Fetched 932 kB in 0s (48.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnmtbnb5y/debhelper_13.31_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.5.4-11 [168 kB] Fetched 168 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2sa041lq/libltdl-dev_2.5.4-11_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 (53.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdoedb7tt/libxml2-16_2.15.2+dfsg-0.1_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/tmp6agds36u/bzip2_1.0.8-6+b1_amd64.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/tmpdt42nfe_/libpam-modules-bin_1.7.0-5+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z unstable/main amd64 mount amd64 2.42-3 [163 kB] Fetched 163 kB in 0s (3770 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjnqh_1ws/mount_2.42-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 patch amd64 2.8-2 [134 kB] Fetched 134 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptb2beiha/patch_2.8-2_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 (128 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8e66t_za/perl-modules-5.40_5.40.1-7_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z unstable/main amd64 libc6-dev amd64 2.42-14 [1992 kB] Fetched 1992 kB in 0s (99.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuya0rgit/libc6-dev_2.42-14_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 (24.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaf54jgk9/libjs-jquery-ui_1.13.2+dfsg-1_all.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 (181 MB/s) dpkg-name: info: moved 'libllvm21_1%3a21.1.8-7_amd64.deb' to '/srv/rebuilderd/tmp/tmpbmenagx1/libllvm21_21.1.8-7_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/tmpkdy5109j/libpciaccess0_0.17-3+b4_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/tmp1ihjytsc/init-system-helpers_1.69_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libncl2 amd64 2.1.21+git20210811.b1213a7-6+b1 [387 kB] Fetched 387 kB in 0s (5261 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdekr0yn5/libncl2_2.1.21+git20210811.b1213a7-6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libprrte-dev amd64 3.0.13-3 [3654 kB] Fetched 3654 kB in 0s (137 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpahq68m1m/libprrte-dev_3.0.13-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bash amd64 5.3-2 [1561 kB] Fetched 1561 kB in 0s (90.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmksuxu6w/bash_5.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z 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/tmp2iofk6p0/libuuid1_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/tmpr_cwzw_5/dh-strip-nondeterminism_1.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-11 [416 kB] Fetched 416 kB in 0s (24.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbwk1b8po/libltdl7_2.5.4-11_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/tmpy9xa0fuc/gcc-16-base_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-11+b1 [709 kB] Fetched 709 kB in 0s (61.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgy0ed6jy/libdb5.3t64_5.3.28+dfsg2-11+b1_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 (453 kB/s) dpkg-name: info: moved 'gcc_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpffacrrpi/gcc_15.2.0-5_amd64.deb' Get: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 (182 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcwssrz_8/gfortran-15-x86-64-linux-gnu_15.2.0-16_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 (37.6 MB/s) dpkg-name: info: moved 'diffutils_1%3a3.12-1_amd64.deb' to '/srv/rebuilderd/tmp/tmplgbn_0u7/diffutils_3.12-1_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 (84.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmwfqzg11/libstdc++-15-dev_15.2.0-16_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 (26.3 MB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpr886vii_/libmagic-mgc_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Fetched 332 kB in 0s (23.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe1_xkbbl/m4_1.4.21-1_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 (7535 kB/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.2-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpo6dfkn72/zlib1g_1.3.dfsg+really1.3.2-3_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 (79.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpglo7azcw/libopenmpi-dev_5.0.10-1_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 (3129 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfvtwxwbl/libnuma-dev_2.0.19-1+b1_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 (7079 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw614rvnk/libsframe3_2.46-3_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 (73.0 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.2-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpb7hozwi7/zlib1g-dev_1.3.dfsg+really1.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsprng2-dev amd64 2.0a-19 [79.3 kB] Fetched 79.3 kB in 0s (1922 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3t261tyr/libsprng2-dev_2.0a-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z unstable/main amd64 libc6 amd64 2.42-14 [1790 kB] Fetched 1790 kB in 0s (106 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb9r9fe5g/libc6_2.42-14_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/tmpenrb1wo_/libdrm-amdgpu1_2.4.131-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg amd64 1.23.7 [1531 kB] Fetched 1531 kB in 0s (90.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcflqosch/dpkg_1.23.7_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 (121 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpog0oca09/cpp-15-x86-64-linux-gnu_15.2.0-16_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 (42.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa9ll0zuh/libdpkg-perl_1.23.7_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libnettle8t64 amd64 3.10.2-1+b1 [305 kB] Fetched 305 kB in 0s (26.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcykb01vz/libnettle8t64_3.10.2-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 grep amd64 3.12-1 [443 kB] Fetched 443 kB in 0s (39.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf1yfbny6/grep_3.12-1_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/tmp0h42zsvx/libquadmath0_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 (115 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3m55_1f8/libgcc-15-dev_15.2.0-16_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/tmpr2c9c5w8/libpkgconf7_2.5.1-4_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 (181 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfjtj6qhg/gcc-15-x86-64-linux-gnu_15.2.0-16_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/tmp6rksaqxf/sensible-utils_0.0.26_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b2 [61.3 kB] Fetched 61.3 kB in 0s (6078 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3n2xs_x0/libevent-openssl-2.1-7t64_2.1.12-stable-10+b2_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/tmpq6o5qtoc/dash_0.5.12-12_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/tmpjjw61or8/librhash1_1.4.6-1.1_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv2bttf17/libnl-3-dev_3.12.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 googletest all 1.17.0-1 [522 kB] Fetched 522 kB in 0s (4089 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpif1kfq0f/googletest_1.17.0-1_all.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/tmprmmzauoa/libldap2_2.6.10+dfsg-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b2 [144 kB] Fetched 144 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplpehxdgu/libxcb1_1.17.0-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.20 [3504 B] Fetched 3504 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_vb_oiyo/mpi-default-dev_1.20_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 (173 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgicu4qn4/libboost1.90-dev_1.90.0-6_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libisl23 amd64 0.27-2 [664 kB] Fetched 664 kB in 0s (51.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpummg8iy5/libisl23_0.27-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z 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/tmp9k4yhe0l/libcap-ng0_0.9.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 base-passwd amd64 3.6.8 [54.6 kB] Fetched 54.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppndtkwmb/base-passwd_3.6.8_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/tmph3fa59ck/libxext6_1.3.4-1+b4_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 (23.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnuoxtivj/libssh2-1t64_1.11.1-2_amd64.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 (3620 kB/s) dpkg-name: info: moved 'libgmpxx4ldbl_2%3a6.3.0+dfsg-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpejz1gjac/libgmpxx4ldbl_6.3.0+dfsg-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.20.1~rc2-1 [955 kB] Fetched 955 kB in 0s (71.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc_dfmpii/libucx0_1.20.1~rc2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssl3t64 amd64 3.6.2-1 [2482 kB] Fetched 2482 kB in 0s (119 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbtnuuxg3/libssl3t64_3.6.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.4.2-1 [480 kB] Fetched 480 kB in 0s (35.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc4oka6s7/libunistring5_1.4.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z 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/tmpa97c4805/libngtcp2-crypto-ossl0_1.21.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphnz4y11y/libarchive-zip-perl_1.68-1_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/tmpqwzcewz0/libedit2_3.1-20251016-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl-base amd64 5.40.1-7+b1 [1676 kB] Fetched 1676 kB in 0s (100 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmbefu8to/perl-base_5.40.1-7+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openssl-provider-legacy amd64 3.6.2-1 [316 kB] Fetched 316 kB in 0s (30.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcb6p8_nu/openssl-provider-legacy_3.6.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Fetched 877 kB in 0s (67.4 MB/s) dpkg-name: info: moved 'automake_1%3a1.18.1-4_all.deb' to '/srv/rebuilderd/tmp/tmpmqnm3js1/automake_1.18.1-4_all.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/tmpu06vux9n/dh-autoreconf_22_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libaudit-common all 1:4.1.2-1 [14.3 kB] Fetched 14.3 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit-common_1%3a4.1.2-1_all.deb' to '/srv/rebuilderd/tmp/tmpen97nblj/libaudit-common_4.1.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsystemd0 amd64 260.1-1 [446 kB] Fetched 446 kB in 0s (41.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk_20o09t/libsystemd0_260.1-1_amd64.deb' Downloading dependency 1 of 270: libmpc3:amd64=1.3.1-3 Downloading dependency 2 of 270: libgfortran5:amd64=16-20260322-1 Downloading dependency 3 of 270: libpam-modules:amd64=1.7.0-5+b1 Downloading dependency 4 of 270: debianutils:amd64=5.23.2 Downloading dependency 5 of 270: dpkg-dev:amd64=1.23.7 Downloading dependency 6 of 270: libcrypt1:amd64=1:4.5.1-1+b1 Downloading dependency 7 of 270: libasan8:amd64=16-20260322-1 Downloading dependency 8 of 270: libseccomp2:amd64=2.6.0-2+b1 Downloading dependency 9 of 270: libblkid1:amd64=2.42-3 Downloading dependency 10 of 270: libgssapi-krb5-2:amd64=1.22.1-2+b1 Downloading dependency 11 of 270: libncl-dev:amd64=2.1.21+git20210811.b1213a7-6+b1 Downloading dependency 12 of 270: libgdbm-compat4t64:amd64=1.26-1+b1 Downloading dependency 13 of 270: pkgconf-bin:amd64=2.5.1-4 Downloading dependency 14 of 270: g++-x86-64-linux-gnu:amd64=4:15.2.0-5 Downloading dependency 15 of 270: libatomic1:amd64=16-20260322-1 Downloading dependency 16 of 270: libxxhash0:amd64=0.8.3-2+b1 Downloading dependency 17 of 270: libmount1:amd64=2.42-3 Downloading dependency 18 of 270: time:amd64=1.9-0.4 Downloading dependency 19 of 270: cpp-15:amd64=15.2.0-16 Downloading dependency 20 of 270: libcurl4t64:amd64=8.20.0~rc2-1 Downloading dependency 21 of 270: libamd-comgr3:amd64=7.0.2+dfsg-3 Downloading dependency 22 of 270: liblzma5:amd64=5.8.3-1 Downloading dependency 23 of 270: libtinfo6:amd64=6.6+20251231-1 Downloading dependency 24 of 270: libacl1:amd64=2.3.2-3 Downloading dependency 25 of 270: autoconf:amd64=2.72-6 Downloading dependency 26 of 270: xz-utils:amd64=5.8.3-1 Downloading dependency 27 of 270: libnuma1:amd64=2.0.19-1+b1 Downloading dependency 28 of 270: libevent-extra-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 29 of 270: libnghttp3-9:amd64=1.15.0-1 Downloading dependency 30 of 270: libgprofng0:amd64=2.46-3 Downloading dependency 31 of 270: liblocale-gettext-perl:amd64=1.07-8 Downloading dependency 32 of 270: libyaml-cpp0.8:amd64=0.8.0+dfsg-9 Downloading dependency 33 of 270: cpp:amd64=4:15.2.0-5 Downloading dependency 34 of 270: gettext:amd64=0.23.2-2 Downloading dependency 35 of 270: libboost-dev:amd64=1.90.0.2 Downloading dependency 36 of 270: libidn2-0:amd64=2.3.8-4+b1 Downloading dependency 37 of 270: gcc-15-base:amd64=15.2.0-16 Downloading dependency 38 of 270: libc-dev-bin:amd64=2.42-14 Downloading dependency 39 of 270: libstdc++6:amd64=16-20260322-1 Downloading dependency 40 of 270: libjsoncpp26:amd64=1.9.6-5+b1 Downloading dependency 41 of 270: libxnvctrl0:amd64=535.171.04-1+b3 Downloading dependency 42 of 270: binutils-common:amd64=2.46-3 Downloading dependency 43 of 270: libibumad3:amd64=61.0-2 Downloading dependency 44 of 270: libjansson4:amd64=2.14-2+b4 Downloading dependency 45 of 270: libsmartcols1:amd64=2.42-3 Downloading dependency 46 of 270: libevent-dev:amd64=2.1.12-stable-10+b2 Downloading dependency 47 of 270: linux-libc-dev:amd64=6.19.12-1 Downloading dependency 48 of 270: libuchardet0:amd64=0.0.8-2+b1 Downloading dependency 49 of 270: libz3-4:amd64=4.13.3-1+b1 Downloading dependency 50 of 270: libtsan2:amd64=16-20260322-1 Downloading dependency 51 of 270: libbinutils:amd64=2.46-3 Downloading dependency 52 of 270: ncurses-base:amd64=6.6+20251231-1 Downloading dependency 53 of 270: libjs-jquery:amd64=3.7.1+dfsg+~3.5.33-1 Downloading dependency 54 of 270: libuv1t64:amd64=1.51.0-2+b1 Downloading dependency 55 of 270: libsepol2:amd64=3.10-1 Downloading dependency 56 of 270: openmpi-bin:amd64=5.0.10-1 Downloading dependency 57 of 270: bsdextrautils:amd64=2.42-3 Downloading dependency 58 of 270: debhelper:amd64=13.31 Downloading dependency 59 of 270: libltdl-dev:amd64=2.5.4-11 Downloading dependency 60 of 270: libxml2-16:amd64=2.15.2+dfsg-0.1 Downloading dependency 61 of 270: bzip2:amd64=1.0.8-6+b1 Downloading dependency 62 of 270: libpam-modules-bin:amd64=1.7.0-5+b1 Downloading dependency 63 of 270: mount:amd64=2.42-3 Downloading dependency 64 of 270: patch:amd64=2.8-2 Downloading dependency 65 of 270: perl-modules-5.40:amd64=5.40.1-7 Downloading dependency 66 of 270: libc6-dev:amd64=2.42-14 Downloading dependency 67 of 270: libjs-jquery-ui:amd64=1.13.2+dfsg-1 Downloading dependency 68 of 270: libllvm21:amd64=1:21.1.8-7 Downloading dependency 69 of 270: libpciaccess0:amd64=0.17-3+b4 Downloading dependency 70 of 270: init-system-helpers:amd64=1.69 Downloading dependency 71 of 270: libncl2:amd64=2.1.21+git20210811.b1213a7-6+b1 Downloading dependency 72 of 270: libprrte-dev:amd64=3.0.13-3 Downloading dependency 73 of 270: bash:amd64=5.3-2 Downloading dependency 74 of 270: libuuid1:amd64=2.42-3 Downloading dependency 75 of 270: dh-strip-nondeterminism:amd64=1.15.0-1 Downloading dependency 76 of 270: libltdl7:amd64=2.5.4-11 Downloading dependency 77 of 270: gcc-16-base:amd64=16-20260322-1 Downloading dependency 78 of 270: libdb5.3t64:amd64=5.3.28+dfsg2-11+b1 Downloading dependency 79 of 270: gcc:amd64=4:15.2.0-5 Downloading dependency 80 of 270: gfortran-15-x86-64-linux-gnu:amd64=15.2.0-16 Downloading dependency 81 of 270: diffutils:amd64=1:3.12-1 Downloading dependency 82 of 270: libstdc++-15-dev:amd64=15.2.0-16 Downloading dependency 83 of 270: libmagic-mgc:amd64=1:5.46-5+b1 Downloading dependency 84 of 270: m4:amd64=1.4.21-1 Downloading dependency 85 of 270: zlib1g:amd64=1:1.3.dfsg+really1.3.2-3 Downloading dependency 86 of 270: libopenmpi-dev:amd64=5.0.10-1 Downloading dependency 87 of 270: libnuma-dev:amd64=2.0.19-1+b1 Downloading dependency 88 of 270: libsframe3:amd64=2.46-3 Downloading dependency 89 of 270: zlib1g-dev:amd64=1:1.3.dfsg+really1.3.2-3 Downloading dependency 90 of 270: libsprng2-dev:amd64=2.0a-19 Downloading dependency 91 of 270: libc6:amd64=2.42-14 Downloading dependency 92 of 270: libdrm-amdgpu1:amd64=2.4.131-1 Downloading dependency 93 of 270: dpkg:amd64=1.23.7 Downloading dependency 94 of 270: cpp-15-x86-64-linux-gnu:amd64=15.2.0-16 Downloading dependency 95 of 270: libdpkg-perl:amd64=1.23.7 Downloading dependency 96 of 270: libnettle8t64:amd64=3.10.2-1+b1 Downloading dependency 97 of 270: grep:amd64=3.12-1 Downloading dependency 98 of 270: libquadmath0:amd64=16-20260322-1 Downloading dependency 99 of 270: libgcc-15-dev:amd64=15.2.0-16 Downloading dependency 100 of 270: libpkgconf7:amd64=2.5.1-4 Downloading dependency 101 of 270: gcc-15-x86-64-linux-gnu:amd64=15.2.0-16 Downloading dependency 102 of 270: sensible-utils:amd64=0.0.26 Downloading dependency 103 of 270: libevent-openssl-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 104 of 270: dash:amd64=0.5.12-12 Downloading dependency 105 of 270: librhash1:amd64=1.4.6-1.1 Downloading dependency 106 of 270: libnl-3-dev:amd64=3.12.0-2 Downloading dependency 107 of 270: googletest:amd64=1.17.0-1 Downloading dependency 108 of 270: libldap2:amd64=2.6.10+dfsg-1+b1 Downloading dependency 109 of 270: libxcb1:amd64=1.17.0-2+b2 Downloading dependency 110 of 270: mpi-default-dev:amd64=1.20 Downloading dependency 111 of 270: libboost1.90-dev:amd64=1.90.0-6 Downloading dependency 112 of 270: libisl23:amd64=0.27-2 Downloading dependency 113 of 270: libcap-ng0:amd64=0.9.2-1 Downloading dependency 114 of 270: base-passwd:amd64=3.6.8 Downloading dependency 115 of 270: libxext6:amd64=2:1.3.4-1+b4 Downloading dependency 116 of 270: libssh2-1t64:amd64=1.11.1-2 Downloading dependency 117 of 270: libgmpxx4ldbl:amd64=2:6.3.0+dfsg-5+b1 Downloading dependency 118 of 270: libucx0:amd64=1.20.1~rc2-1 Downloading dependency 119 of 270: libssl3t64:amd64=3.6.2-1 Downloading dependency 120 of 270: libunistring5:amd64=1.4.2-1 Downloading dependency 121 of 270: libngtcp2-crypto-ossl0:amd64=1.21.0-1 Downloading dependency 122 of 270: libarchive-zip-perl:amd64=1.68-1 Downloading dependency 123 of 270: libedit2:amd64=3.1-20251016-1 Downloading dependency 124 of 270: perl-base:amd64=5.40.1-7+b1 Downloading dependency 125 of 270: openssl-provider-legacy:amd64=3.6.2-1 Downloading dependency 126 of 270: automake:amd64=1:1.18.1-4 Downloading dependency 127 of 270: dh-autoreconf:amd64=22 Downloading dependency 128 of 270: libaudit-common:amd64=1:4.1.2-1 Downloading dependency 129 of 270: libsystemd0:amd64=260.1-1 Downloading dependency 130 of 270: libfabric1:amd64=2.1.0-1.1+b1Get:1 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 2.1.0-1.1+b1 [716 kB] Fetched 716 kB in 0s (55.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpviax9qpq/libfabric1_2.1.0-1.1+b1_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/tmphr4j43bk/libdrm-common_2.4.131-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 systemd amd64 260.1-1 [3299 kB] Fetched 3299 kB in 0s (133 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp98cq02su/systemd_260.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 2.5.1-4 [18.1 kB] Fetched 18.1 kB in 0s (1030 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq6oj3mpq/pkg-config_2.5.1-4_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9lvovq34/libhwloc-plugins_2.13.0-2_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/tmpgk5ieimw/g++-15_15.2.0-16_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwasan0 amd64 16-20260322-1 [1580 kB] Fetched 1580 kB in 0s (93.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5fm1skg3/libhwasan0_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Fetched 22.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp94c3l6mg/intltool-debian_0.35.0+20060710.6_all.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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps1hj4ywp/libnl-route-3-200_3.12.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libperl5.40 amd64 5.40.1-7+b1 [4319 kB] Fetched 4319 kB in 0s (145 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmx92jih6/libperl5.40_5.40.1-7+b1_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 (93.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpthunkozn/man-db_2.13.1-1_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/tmpvfgg0fl0/file_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Fetched 181 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4up0aoc1/libpsm2-2_11.2.185-2.1_amd64.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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp70rheo_m/libfuse3-4_3.18.2-1_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 (42.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpap3if_d8/make_4.4.1-3_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/tmp6ytchc2u/libsasl2-2_2.1.28+dfsg1-11_amd64.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/tmp506oy3k8/libxdmcp6_1.1.5-2_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/tmp61ikm5kt/libgomp1_16-20260322-1_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/tmp2m8_agx3/libkrb5support0_1.22.1-2+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 (48.4 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp1hahug8q/libgmp10_6.3.0+dfsg-5+b1_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 (80.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjrjpisb7/groff-base_1.23.0-10_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/tmpotsuf_ll/gfortran-15_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp30ibcmu4/libprrte-bin_3.0.13-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z unstable/main amd64 libarchive13t64 amd64 3.8.5-1 [362 kB] Fetched 362 kB in 0s (34.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi39jh1le/libarchive13t64_3.8.5-1_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 (31.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2i1znkyo/libkrb5-3_1.22.1-2+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/tmpdk0rtxfk/libcom-err2_1.47.4-1_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 (41.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb1olzf5a/ncurses-bin_6.6+20251231-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z 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/tmp0map821g/autotools-dev_20240727.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblsan0 amd64 16-20260322-1 [1280 kB] Fetched 1280 kB in 0s (81.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2gu1i21_/liblsan0_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Fetched 198 kB in 0s (2840 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpogku_5o1/help2man_1.49.3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 tar amd64 1.35+dfsg-4 [817 kB] Fetched 817 kB in 0s (64.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb7dubxxb/tar_1.35+dfsg-4_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 (15.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptopcof3r/libnl-route-3-dev_3.12.0-2_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/tmpn0klsulq/libdebhelper-perl_13.31_all.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/tmpita0i3om/libnghttp2-14_1.68.1-1_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/tmp_3ez8di7/libpsl5t64_0.21.5-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z unstable/main amd64 libc-gconv-modules-extra amd64 2.42-14 [1094 kB] Fetched 1094 kB in 0s (65.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzj5mxeqb/libc-gconv-modules-extra_2.42-14_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgsi_flkm/libibverbs1_61.0-2_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 (63.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp1wk2hpp/libze1_1.28.2-2_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 (2052 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpplq_z3x9/libsprng2_2.0a-19_amd64.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/tmpongljtb9/libgcc-s1_16-20260322-1_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/tmp_xlz13__/libgdbm6t64_1.26-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z 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/tmp2e1vsp18/libngtcp2-16_1.21.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 binutils amd64 2.46-3 [282 kB] Fetched 282 kB in 0s (27.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyo_umgal/binutils_2.46-3_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/tmpkvjuem7v/hostname_3.25_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/tmp1oina88n/dwz_0.16-4_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 (80.1 MB/s) dpkg-name: info: moved 'passwd_1%3a4.19.3-2_amd64.deb' to '/srv/rebuilderd/tmp/tmpvb_c528a/passwd_4.19.3-2_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 (63.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr6hs1r0j/autopoint_0.23.2-2_all.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/tmp_kjb2j30/build-essential_12.12_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/tmpsd90f3zv/g++_15.2.0-5_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/tmpxaptr47n/libitm1_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Fetched 33.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi8p045sx/pkgconf_2.5.1-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libctf-nobfd0 amd64 2.46-3 [160 kB] Fetched 160 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp312dgw9m/libctf-nobfd0_2.46-3_amd64.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/tmp2bdtfezp/libdrm2_2.4.131-1_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/tmp6w2116nr/libmd0_1.1.0-2+b2_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/tmp8ef_g8ss/libbsd0_0.12.2-2+b1_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp87u1yfi4/libnl-3-200_3.12.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libubsan1 amd64 16-20260322-1 [1136 kB] Fetched 1136 kB in 0s (75.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp17bmxogx/libubsan1_16-20260322-1_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/tmpnij_nmzy/libxau6_1.0.11-1+b1_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/tmpwfs0gxhl/po-debconf_1.0.22_all.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/tmp8hmmgrtj/libevent-2.1-7t64_2.1.12-stable-10+b2_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 (33.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpajn_7ekj/gcc-15_15.2.0-16_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:10.3p1-1 [1003 kB] Fetched 1003 kB in 0s (73.3 MB/s) dpkg-name: info: moved 'openssh-client_1%3a10.3p1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpfd4ib5zw/openssh-client_10.3p1-1_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/tmpntkwyw7f/libevent-core-2.1-7t64_2.1.12-stable-10+b2_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 (60.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9ers9vyl/libmpfr6_4.2.2-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z unstable/main amd64 util-linux amd64 2.42-3 [1221 kB] Fetched 1221 kB in 0s (83.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjgt7ptuh/util-linux_2.42-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sed amd64 4.9-2 [329 kB] Fetched 329 kB in 0s (31.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpevz5qxb2/sed_4.9-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 adduser all 3.155 [212 kB] Fetched 212 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo_jm44f_/adduser_3.155_all.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/tmp6r8xzx4a/libudev1_260.1-1_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 (64.2 MB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.13-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpgmaq6v1f/libx11-6_1.8.13-1_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 (62.0 MB/s) dpkg-name: info: moved 'libclang-common-21-dev_1%3a21.1.8-7_amd64.deb' to '/srv/rebuilderd/tmp/tmpnqr9w6ee/libclang-common-21-dev_21.1.8-7_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 (171 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpil7147kx/libamdhip64-6_6.4.3-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-4 [25.2 kB] Fetched 25.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvd0yur36/libffi8_3.5.2-4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libucc1 amd64 1.7.0~rc1-1 [329 kB] Fetched 329 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd5f723l2/libucc1_1.7.0~rc1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libaudit1 amd64 1:4.1.2-1+b1 [60.2 kB] Fetched 60.2 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit1_1%3a4.1.2-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpfqznk1l8/libaudit1_4.1.2-1+b1_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9u8txpix/libcbor0.10_0.10.2-2.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.10-1 [30.3 kB] Fetched 30.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpybmd4gvn/openmpi-common_5.0.10-1_all.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/tmp5e881dcp/libk5crypto3_1.22.1-2+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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps0rgy1lu/rpcsvc-proto_1.4.3-1_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/tmpdix94_j6/sysvinit-utils_3.18-1_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 (4728 kB/s) dpkg-name: info: moved 'libgmp-dev_2%3a6.3.0+dfsg-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp4c8g515q/libgmp-dev_6.3.0+dfsg-5+b1_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 (64.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd8_ydnsd/libgfortran-15-dev_15.2.0-16_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260418T022809Z unstable/main amd64 libc-bin amd64 2.42-14 [621 kB] Fetched 621 kB in 0s (53.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl3qsfo2u/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/tmpad5a2r_w/libelf1t64_0.194-4_amd64.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/tmpg_zf7tw2/libdebconfclient0_0.282+b2_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/tmpql9dqnaq/libpcre2-8-0_10.46-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-11 [17.2 kB] Fetched 17.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc6hofl4v/libsasl2-modules-db_2.1.28+dfsg1-11_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 (119 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeif4lgvr/libsystemd-shared_260.1-1_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/tmpqmxhn50v/libbz2-1.0_1.0.8-6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.4~rc3-5 [500 kB] Fetched 500 kB in 0s (6585 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp49rws09l/libsimde-dev_0.8.4~rc3-5_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 (29.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp473587h7/libzstd1_1.5.7+dfsg-3+b1_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 (1147 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp86uprt15/ocl-icd-libopencl1_2.3.4-1_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 (181 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdwg27izm/g++-15-x86-64-linux-gnu_15.2.0-16_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 (56.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2lnesswi/libibverbs-dev_61.0-2_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv5537gnj/libhwloc-dev_2.13.0-2_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/tmp2cpvc0_d/libevent-pthreads-2.1-7t64_2.1.12-stable-10+b2_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/tmpyutoy291/libbrotli1_1.2.0-3_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/tmpb6zqpevm/base-files_14_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/tmpwqs8wl5t/debconf_1.5.92_all.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/tmpbkp0hkbh/libexpat1_2.7.5-1_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/tmpp9luljye/libfile-stripnondeterminism-perl_1.15.0-1_all.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 (76.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1y355vet/binutils-x86-64-linux-gnu_2.46-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.4.3+dfsg-5 [678 kB] Fetched 678 kB in 0s (56.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi_zbmsw5/libhsa-runtime64-1_6.4.3+dfsg-5_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/tmpxyeovm7l/libctf0_2.46-3_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/tmphgzz5xm7/libpam0g_1.7.0-5+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 (34.5 MB/s) dpkg-name: info: moved 'libx11-data_2%3a1.8.13-1_all.deb' to '/srv/rebuilderd/tmp/tmp22gi3l52/libx11-data_1.8.13-1_all.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 (0 B/s) dpkg-name: info: moved 'login.defs_1%3a4.19.3-2_all.deb' to '/srv/rebuilderd/tmp/tmpen842nf3/login.defs_4.19.3-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.10-1 [2018 kB] Fetched 2018 kB in 0s (108 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq6fg3s5d/libopenmpi40_5.0.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-runtime all 1.7.0-5 [249 kB] Fetched 249 kB in 0s (24.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplbailzk9/libpam-runtime_1.7.0-5_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 (39.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphy2uip39/libprrte3_3.0.13-3_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4nnvlgwa/libsemanage-common_3.10-1_all.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/tmp229npjqe/mawk_1.3.4.20260302-1_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 (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp58dbejqe/librdmacm1t64_61.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-5 [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/tmpebnp2l7z/gcc-x86-64-linux-gnu_15.2.0-5_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 (4608 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplt6i66z7/libpipeline1_1.5.8-2+b1_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 (184 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6z4g75p2/cmake_4.3.1-1_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 (7288 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpndt_3yc7/libyaml-cpp-dev_0.8.0+dfsg-9_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/tmpq1i7hys9/libcc1-0_16-20260322-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libselinux1 amd64 3.10-1 [85.4 kB] Fetched 85.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsg67d14c/libselinux1_3.10-1_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 (62.8 MB/s) dpkg-name: info: moved 'procps_2%3a4.0.4-9+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmphz1hacmu/procps_4.0.4-9+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Fetched 539 kB in 0s (46.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd0i_zdtp/libtool_2.5.4-11_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.13.0-2 [165 kB] Fetched 165 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprt3vos93/libhwloc15_2.13.0-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gzip amd64 1.13-1 [138 kB] Fetched 138 kB in 0s (13.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk4603fl9/gzip_1.13-1_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/tmpfkx9ypkc/libproc2-0_4.0.4-9+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 chrpath amd64 0.18-1 [13.5 kB] Fetched 13.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6w3lzvx_/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/tmp5tha_39m/libkeyutils1_1.6.3-6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 61.0-2 [381 kB] Fetched 381 kB in 0s (36.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmbxp_a95/ibverbs-providers_61.0-2_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 (26.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppskwnqkr/libeigen3-dev_3.4.0-5_all.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/tmp1y98nghr/libmagic1t64_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.18-1 [18.8 kB] Fetched 18.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuanhco89/libmunge2_0.5.18-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libattr1 amd64 1:2.5.2-4 [23.0 kB] Fetched 23.0 kB in 0s (0 B/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpm4q72olc/libattr1_2.5.2-4_amd64.deb' Downloading dependency 131 of 270: libdrm-common:amd64=2.4.131-1 Downloading dependency 132 of 270: systemd:amd64=260.1-1 Downloading dependency 133 of 270: pkg-config:amd64=2.5.1-4 Downloading dependency 134 of 270: libhwloc-plugins:amd64=2.13.0-2 Downloading dependency 135 of 270: g++-15:amd64=15.2.0-16 Downloading dependency 136 of 270: libhwasan0:amd64=16-20260322-1 Downloading dependency 137 of 270: intltool-debian:amd64=0.35.0+20060710.6 Downloading dependency 138 of 270: libnl-route-3-200:amd64=3.12.0-2 Downloading dependency 139 of 270: libperl5.40:amd64=5.40.1-7+b1 Downloading dependency 140 of 270: man-db:amd64=2.13.1-1 Downloading dependency 141 of 270: file:amd64=1:5.46-5+b1 Downloading dependency 142 of 270: libpsm2-2:amd64=11.2.185-2.1 Downloading dependency 143 of 270: libfuse3-4:amd64=3.18.2-1 Downloading dependency 144 of 270: make:amd64=4.4.1-3 Downloading dependency 145 of 270: libsasl2-2:amd64=2.1.28+dfsg1-11 Downloading dependency 146 of 270: libxdmcp6:amd64=1:1.1.5-2 Downloading dependency 147 of 270: libgomp1:amd64=16-20260322-1 Downloading dependency 148 of 270: libkrb5support0:amd64=1.22.1-2+b1 Downloading dependency 149 of 270: libgmp10:amd64=2:6.3.0+dfsg-5+b1 Downloading dependency 150 of 270: groff-base:amd64=1.23.0-10 Downloading dependency 151 of 270: gfortran-15:amd64=15.2.0-16 Downloading dependency 152 of 270: libprrte-bin:amd64=3.0.13-3 Downloading dependency 153 of 270: libarchive13t64:amd64=3.8.5-1 Downloading dependency 154 of 270: libkrb5-3:amd64=1.22.1-2+b1 Downloading dependency 155 of 270: libcom-err2:amd64=1.47.4-1 Downloading dependency 156 of 270: ncurses-bin:amd64=6.6+20251231-1 Downloading dependency 157 of 270: autotools-dev:amd64=20240727.1 Downloading dependency 158 of 270: liblsan0:amd64=16-20260322-1 Downloading dependency 159 of 270: help2man:amd64=1.49.3 Downloading dependency 160 of 270: tar:amd64=1.35+dfsg-4 Downloading dependency 161 of 270: libnl-route-3-dev:amd64=3.12.0-2 Downloading dependency 162 of 270: libdebhelper-perl:amd64=13.31 Downloading dependency 163 of 270: libnghttp2-14:amd64=1.68.1-1 Downloading dependency 164 of 270: libpsl5t64:amd64=0.21.5-1 Downloading dependency 165 of 270: libc-gconv-modules-extra:amd64=2.42-14 Downloading dependency 166 of 270: libibverbs1:amd64=61.0-2 Downloading dependency 167 of 270: libze1:amd64=1.28.2-2 Downloading dependency 168 of 270: libsprng2:amd64=2.0a-19 Downloading dependency 169 of 270: libgcc-s1:amd64=16-20260322-1 Downloading dependency 170 of 270: libgdbm6t64:amd64=1.26-1+b1 Downloading dependency 171 of 270: libngtcp2-16:amd64=1.21.0-1 Downloading dependency 172 of 270: binutils:amd64=2.46-3 Downloading dependency 173 of 270: hostname:amd64=3.25 Downloading dependency 174 of 270: dwz:amd64=0.16-4 Downloading dependency 175 of 270: passwd:amd64=1:4.19.3-2 Downloading dependency 176 of 270: autopoint:amd64=0.23.2-2 Downloading dependency 177 of 270: build-essential:amd64=12.12 Downloading dependency 178 of 270: g++:amd64=4:15.2.0-5 Downloading dependency 179 of 270: libitm1:amd64=16-20260322-1 Downloading dependency 180 of 270: pkgconf:amd64=2.5.1-4 Downloading dependency 181 of 270: libctf-nobfd0:amd64=2.46-3 Downloading dependency 182 of 270: libdrm2:amd64=2.4.131-1 Downloading dependency 183 of 270: libmd0:amd64=1.1.0-2+b2 Downloading dependency 184 of 270: libbsd0:amd64=0.12.2-2+b1 Downloading dependency 185 of 270: libnl-3-200:amd64=3.12.0-2 Downloading dependency 186 of 270: libubsan1:amd64=16-20260322-1 Downloading dependency 187 of 270: libxau6:amd64=1:1.0.11-1+b1 Downloading dependency 188 of 270: po-debconf:amd64=1.0.22 Downloading dependency 189 of 270: libevent-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 190 of 270: gcc-15:amd64=15.2.0-16 Downloading dependency 191 of 270: openssh-client:amd64=1:10.3p1-1 Downloading dependency 192 of 270: libevent-core-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 193 of 270: libmpfr6:amd64=4.2.2-3 Downloading dependency 194 of 270: util-linux:amd64=2.42-3 Downloading dependency 195 of 270: sed:amd64=4.9-2 Downloading dependency 196 of 270: adduser:amd64=3.155 Downloading dependency 197 of 270: libudev1:amd64=260.1-1 Downloading dependency 198 of 270: libx11-6:amd64=2:1.8.13-1 Downloading dependency 199 of 270: libclang-common-21-dev:amd64=1:21.1.8-7 Downloading dependency 200 of 270: libamdhip64-6:amd64=6.4.3-5 Downloading dependency 201 of 270: libffi8:amd64=3.5.2-4 Downloading dependency 202 of 270: libucc1:amd64=1.7.0~rc1-1 Downloading dependency 203 of 270: libaudit1:amd64=1:4.1.2-1+b1 Downloading dependency 204 of 270: libcbor0.10:amd64=0.10.2-2.1 Downloading dependency 205 of 270: openmpi-common:amd64=5.0.10-1 Downloading dependency 206 of 270: libk5crypto3:amd64=1.22.1-2+b1 Downloading dependency 207 of 270: rpcsvc-proto:amd64=1.4.3-1 Downloading dependency 208 of 270: sysvinit-utils:amd64=3.18-1 Downloading dependency 209 of 270: libgmp-dev:amd64=2:6.3.0+dfsg-5+b1 Downloading dependency 210 of 270: libgfortran-15-dev:amd64=15.2.0-16 Downloading dependency 211 of 270: libc-bin:amd64=2.42-14 Downloading dependency 212 of 270: libelf1t64:amd64=0.194-4 Downloading dependency 213 of 270: libdebconfclient0:amd64=0.282+b2 Downloading dependency 214 of 270: libpcre2-8-0:amd64=10.46-1+b1 Downloading dependency 215 of 270: libsasl2-modules-db:amd64=2.1.28+dfsg1-11 Downloading dependency 216 of 270: libsystemd-shared:amd64=260.1-1 Downloading dependency 217 of 270: libbz2-1.0:amd64=1.0.8-6+b1 Downloading dependency 218 of 270: libsimde-dev:amd64=0.8.4~rc3-5 Downloading dependency 219 of 270: libzstd1:amd64=1.5.7+dfsg-3+b1 Downloading dependency 220 of 270: ocl-icd-libopencl1:amd64=2.3.4-1 Downloading dependency 221 of 270: g++-15-x86-64-linux-gnu:amd64=15.2.0-16 Downloading dependency 222 of 270: libibverbs-dev:amd64=61.0-2 Downloading dependency 223 of 270: libhwloc-dev:amd64=2.13.0-2 Downloading dependency 224 of 270: libevent-pthreads-2.1-7t64:amd64=2.1.12-stable-10+b2 Downloading dependency 225 of 270: libbrotli1:amd64=1.2.0-3 Downloading dependency 226 of 270: base-files:amd64=14 Downloading dependency 227 of 270: debconf:amd64=1.5.92 Downloading dependency 228 of 270: libexpat1:amd64=2.7.5-1 Downloading dependency 229 of 270: libfile-stripnondeterminism-perl:amd64=1.15.0-1 Downloading dependency 230 of 270: binutils-x86-64-linux-gnu:amd64=2.46-3 Downloading dependency 231 of 270: libhsa-runtime64-1:amd64=6.4.3+dfsg-5 Downloading dependency 232 of 270: libctf0:amd64=2.46-3 Downloading dependency 233 of 270: libpam0g:amd64=1.7.0-5+b1 Downloading dependency 234 of 270: libx11-data:amd64=2:1.8.13-1 Downloading dependency 235 of 270: login.defs:amd64=1:4.19.3-2 Downloading dependency 236 of 270: libopenmpi40:amd64=5.0.10-1 Downloading dependency 237 of 270: libpam-runtime:amd64=1.7.0-5 Downloading dependency 238 of 270: libprrte3:amd64=3.0.13-3 Downloading dependency 239 of 270: libsemanage-common:amd64=3.10-1 Downloading dependency 240 of 270: mawk:amd64=1.3.4.20260302-1 Downloading dependency 241 of 270: librdmacm1t64:amd64=61.0-2 Downloading dependency 242 of 270: gcc-x86-64-linux-gnu:amd64=4:15.2.0-5 Downloading dependency 243 of 270: libpipeline1:amd64=1.5.8-2+b1 Downloading dependency 244 of 270: cmake:amd64=4.3.1-1 Downloading dependency 245 of 270: libyaml-cpp-dev:amd64=0.8.0+dfsg-9 Downloading dependency 246 of 270: libcc1-0:amd64=16-20260322-1 Downloading dependency 247 of 270: libselinux1:amd64=3.10-1 Downloading dependency 248 of 270: procps:amd64=2:4.0.4-9+b1 Downloading dependency 249 of 270: libtool:amd64=2.5.4-11 Downloading dependency 250 of 270: libhwloc15:amd64=2.13.0-2 Downloading dependency 251 of 270: gzip:amd64=1.13-1 Downloading dependency 252 of 270: libproc2-0:amd64=2:4.0.4-9+b1 Downloading dependency 253 of 270: chrpath:amd64=0.18-1 Downloading dependency 254 of 270: libkeyutils1:amd64=1.6.3-6+b1 Downloading dependency 255 of 270: ibverbs-providers:amd64=61.0-2 Downloading dependency 256 of 270: libeigen3-dev:amd64=3.4.0-5 Downloading dependency 257 of 270: libmagic1t64:amd64=1:5.46-5+b1 Downloading dependency 258 of 270: libmunge2:amd64=0.5.18-1 Downloading dependency 259 of 270: libattr1:amd64=1:2.5.2-4 Downloading dependency 260 of 270: libibmad5:amd64=61.0-2Get:1 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 61.0-2 [44.9 kB] Fetched 44.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_nskg0nd/libibmad5_61.0-2_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/tmp7kke6nu6/gettext-base_0.23.2-2_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/tmpfgamrjz2/libncursesw6_6.6+20251231-1_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 (56.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcpb_vitr/findutils_4.10.0-3_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 (57.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps3ieavj1/libpmix2t64_6.0.0+really5.0.9-3_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 (7229 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplbe3ug5s/libsemanage2_3.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl amd64 5.40.1-7+b1 [264 kB] Fetched 264 kB in 0s (26.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4tomymam/perl_5.40.1-7+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/tmpmf3vsjhp/cpp-x86-64-linux-gnu_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 coreutils amd64 9.10-1 [3142 kB] Fetched 3142 kB in 0s (127 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt3iiw0us/coreutils_9.10-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.17.0-1 [80.6 kB] Fetched 80.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsq26kbvw/libfido2-1_1.17.0-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblz4-1 amd64 1.10.0-9 [70.3 kB] Fetched 70.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2bb_3sit/liblz4-1_1.10.0-9_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/tmpiopvzvfn/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.5uCs7jIffE as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.5uCs7jIffE 127.0.0.1 - - [20/Apr/2026 19:43:19] code 404, message File not found 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:34481 ./ InRelease 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:34481 ./ Release [462 B] 127.0.0.1 - - [20/Apr/2026 19:43:19] code 404, message File not found 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:34481 ./ Release.gpg 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:34481 ./ Packages [334 kB] Fetched 334 kB in 0s (19.7 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 - - [20/Apr/2026 19:43:19] "GET /./gcc-16-base_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libc-gconv-modules-extra_2.42-14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libc6_2.42-14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libgcc-s1_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./mawk_1.3.4.20260302-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./base-files_14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libtinfo6_6.6%2b20251231-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./debianutils_5.23.2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./bash_5.3-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libacl1_2.3.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libattr1_2.5.2-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libgmp10_6.3.0%2bdfsg-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libpcre2-8-0_10.46-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libselinux1_3.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libzstd1_1.5.7%2bdfsg-3%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./zlib1g_1.3.dfsg%2breally1.3.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libssl3t64_3.6.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./openssl-provider-legacy_3.6.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libsystemd0_260.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./coreutils_9.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./dash_0.5.12-12_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./diffutils_3.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libbz2-1.0_1.0.8-6%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./liblzma5_5.8.3-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libmd0_1.1.0-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./tar_1.35%2bdfsg-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./dpkg_1.23.7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./findutils_4.10.0-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./grep_3.12-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./gzip_1.13-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./hostname_3.25_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./ncurses-bin_6.6%2b20251231-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libcrypt1_4.5.1-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./perl-base_5.40.1-7%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./sed_4.9-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libaudit-common_4.1.2-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libcap-ng0_0.9.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libaudit1_4.1.2-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libdb5.3t64_5.3.28%2bdfsg2-11%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./debconf_1.5.92_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libpam0g_1.7.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libpam-modules-bin_1.7.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libpam-modules_1.7.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libpam-runtime_1.7.0-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libblkid1_2.42-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libmount1_2.42-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libsmartcols1_2.42-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libudev1_260.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libuuid1_2.42-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./util-linux_2.42-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libdebconfclient0_0.282%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./base-passwd_3.6.8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./init-system-helpers_1.69_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./libc-bin_2.42-14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "GET /./ncurses-base_6.6%2b20251231-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:19] "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.5uCs7jIffE 127.0.0.1 - - [20/Apr/2026 19:43:20] code 404, message File not found 127.0.0.1 - - [20/Apr/2026 19:43:20] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:34481 ./ InRelease 127.0.0.1 - - [20/Apr/2026 19:43:20] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:34481 ./ Release 127.0.0.1 - - [20/Apr/2026 19:43:20] code 404, message File not found 127.0.0.1 - - [20/Apr/2026 19:43:20] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:34481 ./ 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.5uCs7jIffE 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 - - [20/Apr/2026 19:43:36] "GET /./liblocale-gettext-perl_1.07-8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./mount_2.42-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libsystemd-shared_260.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./systemd_260.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libexpat1_2.7.5-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./login.defs_4.19.3-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libbsd0_0.12.2-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libsemanage-common_3.10-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libsepol2_3.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libsemanage2_3.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./passwd_4.19.3-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./sensible-utils_0.0.26_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./adduser_3.155_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libstdc%2b%2b6_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libuchardet0_0.0.8-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./groff-base_1.23.0-10_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./bsdextrautils_2.42-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libgdbm6t64_1.26-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libpipeline1_1.5.8-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libseccomp2_2.6.0-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./man-db_2.13.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libncursesw6_6.6%2b20251231-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libproc2-0_4.0.4-9%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./procps_4.0.4-9%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./bzip2_1.0.8-6%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libmagic-mgc_5.46-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libmagic1t64_5.46-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./file_5.46-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./gettext-base_0.23.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libedit2_3.1-20251016-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libcbor0.10_0.10.2-2.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libfido2-1_1.17.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libkrb5support0_1.22.1-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libcom-err2_1.47.4-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libk5crypto3_1.22.1-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libkeyutils1_1.6.3-6%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:36] "GET /./libkrb5-3_1.22.1-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libgssapi-krb5-2_1.22.1-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./openssh-client_10.3p1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./perl-modules-5.40_5.40.1-7_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libgdbm-compat4t64_1.26-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libperl5.40_5.40.1-7%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./perl_5.40.1-7%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./xz-utils_5.8.3-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./m4_1.4.21-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./autoconf_2.72-6_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./autotools-dev_20240727.1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./automake_1.18.1-4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./autopoint_0.23.2-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libsframe3_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./binutils-common_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libbinutils_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libgprofng0_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libctf-nobfd0_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libctf0_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libjansson4_2.14-2%2bb4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./binutils-x86-64-linux-gnu_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./binutils_2.46-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libc-dev-bin_2.42-14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./linux-libc-dev_6.19.12-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./rpcsvc-proto_1.4.3-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libc6-dev_2.42-14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./gcc-15-base_15.2.0-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libisl23_0.27-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libmpfr6_4.2.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libmpc3_1.3.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./cpp-15-x86-64-linux-gnu_15.2.0-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./cpp-15_15.2.0-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./cpp-x86-64-linux-gnu_15.2.0-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./cpp_15.2.0-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libcc1-0_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libgomp1_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libitm1_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libatomic1_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libasan8_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./liblsan0_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libtsan2_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libubsan1_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libhwasan0_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libquadmath0_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libgcc-15-dev_15.2.0-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./gcc-15-x86-64-linux-gnu_15.2.0-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./gcc-15_15.2.0-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./gcc-x86-64-linux-gnu_15.2.0-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./gcc_15.2.0-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libstdc%2b%2b-15-dev_15.2.0-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./g%2b%2b-15-x86-64-linux-gnu_15.2.0-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./g%2b%2b-15_15.2.0-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./g%2b%2b-x86-64-linux-gnu_15.2.0-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./g%2b%2b_15.2.0-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./make_4.4.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libdpkg-perl_1.23.7_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./patch_2.8-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./dpkg-dev_1.23.7_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./build-essential_12.12_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./chrpath_0.18-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libxxhash0_0.8.3-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./liblz4-1_1.10.0-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libnettle8t64_3.10.2-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libxml2-16_2.15.2%2bdfsg-0.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libarchive13t64_3.8.5-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libnghttp3-9_1.15.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libngtcp2-16_1.21.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libbrotli1_1.2.0-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libunistring5_1.4.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libidn2-0_2.3.8-4%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libsasl2-modules-db_2.1.28%2bdfsg1-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libsasl2-2_2.1.28%2bdfsg1-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libldap2_2.6.10%2bdfsg-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libnghttp2-14_1.68.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libngtcp2-crypto-ossl0_1.21.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libpsl5t64_0.21.5-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libssh2-1t64_1.11.1-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libcurl4t64_8.20.0%7erc2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libjsoncpp26_1.9.6-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./librhash1_1.4.6-1.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libuv1t64_1.51.0-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./cmake_4.3.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libdebhelper-perl_13.31_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libtool_2.5.4-11_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./dh-autoreconf_22_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libarchive-zip-perl_1.68-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libfile-stripnondeterminism-perl_1.15.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./dh-strip-nondeterminism_1.15.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libelf1t64_0.194-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./dwz_0.16-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./gettext_0.23.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./intltool-debian_0.35.0%2b20060710.6_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./po-debconf_1.0.22_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./debhelper_13.31_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:37] "GET /./libgfortran5_16-20260322-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libncl2_2.1.21%2bgit20210811.b1213a7-6%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libncl-dev_2.1.21%2bgit20210811.b1213a7-6%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libpkgconf7_2.5.1-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./pkgconf-bin_2.5.1-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./time_1.9-0.4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libffi8_3.5.2-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libz3-4_4.13.3-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libllvm21_21.1.8-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libclang-common-21-dev_21.1.8-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libamd-comgr3_7.0.2%2bdfsg-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libnuma1_2.0.19-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libevent-core-2.1-7t64_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libevent-extra-2.1-7t64_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libyaml-cpp0.8_0.8.0%2bdfsg-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libboost1.90-dev_1.90.0-6_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libboost-dev_1.90.0.2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libxau6_1.0.11-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libxdmcp6_1.1.5-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libxcb1_1.17.0-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libx11-data_1.8.13-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libx11-6_1.8.13-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libxext6_1.3.4-1%2bb4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libxnvctrl0_535.171.04-1%2bb3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libibumad3_61.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libevent-2.1-7t64_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libevent-pthreads-2.1-7t64_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libevent-openssl-2.1-7t64_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libevent-dev_2.1.12-stable-10%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libjs-jquery_3.7.1%2bdfsg%2b%7e3.5.33-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libnl-3-200_3.12.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libnl-route-3-200_3.12.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libibverbs1_61.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./ibverbs-providers_61.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libpsm2-2_11.2.185-2.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./librdmacm1t64_61.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libfabric1_2.1.0-1.1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libhwloc15_2.13.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libmunge2_0.5.18-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libpciaccess0_0.17-3%2bb4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libze1_1.28.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./ocl-icd-libopencl1_2.3.4-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libhwloc-plugins_2.13.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libpmix2t64_6.0.0%2breally5.0.9-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libdrm-common_2.4.131-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libdrm2_2.4.131-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libdrm-amdgpu1_2.4.131-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libhsa-runtime64-1_6.4.3%2bdfsg-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libamdhip64-6_6.4.3-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libfuse3-4_3.18.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libibmad5_61.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libucx0_1.20.1%7erc2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libucc1_1.7.0%7erc1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libopenmpi40_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./openmpi-common_5.0.10-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libprrte3_3.0.13-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libprrte-bin_3.0.13-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./openmpi-bin_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libltdl7_2.5.4-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libltdl-dev_2.5.4-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libjs-jquery-ui_1.13.2%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libprrte-dev_3.0.13-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libgfortran-15-dev_15.2.0-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./gfortran-15-x86-64-linux-gnu_15.2.0-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./gfortran-15_15.2.0-16_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libnl-3-dev_3.12.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libnl-route-3-dev_3.12.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libibverbs-dev_61.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libnuma-dev_2.0.19-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libhwloc-dev_2.13.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./zlib1g-dev_1.3.dfsg%2breally1.3.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libopenmpi-dev_5.0.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libsprng2_2.0a-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libgmpxx4ldbl_6.3.0%2bdfsg-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libgmp-dev_6.3.0%2bdfsg-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libsprng2-dev_2.0a-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./googletest_1.17.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./mpi-default-dev_1.20_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./pkgconf_2.5.1-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./help2man_1.49.3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libsimde-dev_0.8.4%7erc3-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libyaml-cpp-dev_0.8.0%2bdfsg-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./libeigen3-dev_3.4.0-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [20/Apr/2026 19:43:38] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmpiopvzvfn/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.5uCs7jIffE Reading package lists... Building dependency tree... Reading state information... libmpc3 is already the newest version (1.3.1-3). libmpc3 set to manually installed. libgfortran5 is already the newest version (16-20260322-1). libgfortran5 set to manually installed. libpam-modules is already the newest version (1.7.0-5+b1). debianutils is already the newest version (5.23.2). dpkg-dev is already the newest version (1.23.7). dpkg-dev set to manually installed. libcrypt1 is already the newest version (1:4.5.1-1+b1). libasan8 is already the newest version (16-20260322-1). libasan8 set to manually installed. libseccomp2 is already the newest version (2.6.0-2+b1). libseccomp2 set to manually installed. libblkid1 is already the newest version (2.42-3). libgssapi-krb5-2 is already the newest version (1.22.1-2+b1). libgssapi-krb5-2 set to manually installed. libncl-dev is already the newest version (2.1.21+git20210811.b1213a7-6+b1). libncl-dev set to manually installed. libgdbm-compat4t64 is already the newest version (1.26-1+b1). libgdbm-compat4t64 set to manually installed. pkgconf-bin is already the newest version (2.5.1-4). pkgconf-bin 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. libatomic1 is already the newest version (16-20260322-1). libatomic1 set to manually installed. libxxhash0 is already the newest version (0.8.3-2+b1). libxxhash0 set to manually installed. libmount1 is already the newest version (2.42-3). time is already the newest version (1.9-0.4). time set to manually installed. cpp-15 is already the newest version (15.2.0-16). cpp-15 set to manually installed. libcurl4t64 is already the newest version (8.20.0~rc2-1). libcurl4t64 set to manually installed. libamd-comgr3 is already the newest version (7.0.2+dfsg-3). libamd-comgr3 set to manually installed. liblzma5 is already the newest version (5.8.3-1). libtinfo6 is already the newest version (6.6+20251231-1). libacl1 is already the newest version (2.3.2-3). autoconf is already the newest version (2.72-6). autoconf set to manually installed. xz-utils is already the newest version (5.8.3-1). xz-utils set to manually installed. libnuma1 is already the newest version (2.0.19-1+b1). libnuma1 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. libnghttp3-9 is already the newest version (1.15.0-1). libnghttp3-9 set to manually installed. libgprofng0 is already the newest version (2.46-3). libgprofng0 set to manually installed. liblocale-gettext-perl is already the newest version (1.07-8). liblocale-gettext-perl set to manually installed. libyaml-cpp0.8 is already the newest version (0.8.0+dfsg-9). libyaml-cpp0.8 set to manually installed. cpp is already the newest version (4:15.2.0-5). cpp set to manually installed. gettext is already the newest version (0.23.2-2). gettext set to manually installed. libboost-dev is already the newest version (1.90.0.2). libboost-dev set to manually installed. libidn2-0 is already the newest version (2.3.8-4+b1). libidn2-0 set to manually installed. gcc-15-base is already the newest version (15.2.0-16). gcc-15-base set to manually installed. libc-dev-bin is already the newest version (2.42-14). libc-dev-bin set to manually installed. libstdc++6 is already the newest version (16-20260322-1). libstdc++6 set to manually installed. libjsoncpp26 is already the newest version (1.9.6-5+b1). libjsoncpp26 set to manually installed. libxnvctrl0 is already the newest version (535.171.04-1+b3). libxnvctrl0 set to manually installed. binutils-common is already the newest version (2.46-3). binutils-common set to manually installed. libibumad3 is already the newest version (61.0-2). libibumad3 set to manually installed. libjansson4 is already the newest version (2.14-2+b4). libjansson4 set to manually installed. libsmartcols1 is already the newest version (2.42-3). libevent-dev is already the newest version (2.1.12-stable-10+b2). libevent-dev set to manually installed. linux-libc-dev is already the newest version (6.19.12-1). linux-libc-dev set to manually installed. libuchardet0 is already the newest version (0.0.8-2+b1). libuchardet0 set to manually installed. libz3-4 is already the newest version (4.13.3-1+b1). libz3-4 set to manually installed. libtsan2 is already the newest version (16-20260322-1). libtsan2 set to manually installed. libbinutils is already the newest version (2.46-3). libbinutils set to manually installed. ncurses-base is already the newest version (6.6+20251231-1). libjs-jquery is already the newest version (3.7.1+dfsg+~3.5.33-1). libjs-jquery set to manually installed. libuv1t64 is already the newest version (1.51.0-2+b1). libuv1t64 set to manually installed. libsepol2 is already the newest version (3.10-1). libsepol2 set to manually installed. openmpi-bin is already the newest version (5.0.10-1). openmpi-bin set to manually installed. bsdextrautils is already the newest version (2.42-3). bsdextrautils set to manually installed. debhelper is already the newest version (13.31). debhelper set to manually installed. libltdl-dev is already the newest version (2.5.4-11). libltdl-dev set to manually installed. libxml2-16 is already the newest version (2.15.2+dfsg-0.1). libxml2-16 set to manually installed. bzip2 is already the newest version (1.0.8-6+b1). bzip2 set to manually installed. libpam-modules-bin is already the newest version (1.7.0-5+b1). mount is already the newest version (2.42-3). mount set to manually installed. patch is already the newest version (2.8-2). patch set to manually installed. perl-modules-5.40 is already the newest version (5.40.1-7). perl-modules-5.40 set to manually installed. libc6-dev is already the newest version (2.42-14). libc6-dev set to manually installed. libjs-jquery-ui is already the newest version (1.13.2+dfsg-1). libjs-jquery-ui set to manually installed. libllvm21 is already the newest version (1:21.1.8-7). libllvm21 set to manually installed. libpciaccess0 is already the newest version (0.17-3+b4). libpciaccess0 set to manually installed. init-system-helpers is already the newest version (1.69). libncl2 is already the newest version (2.1.21+git20210811.b1213a7-6+b1). libncl2 set to manually installed. libprrte-dev is already the newest version (3.0.13-3). libprrte-dev set to manually installed. bash is already the newest version (5.3-2). libuuid1 is already the newest version (2.42-3). dh-strip-nondeterminism is already the newest version (1.15.0-1). dh-strip-nondeterminism set to manually installed. libltdl7 is already the newest version (2.5.4-11). libltdl7 set to manually installed. gcc-16-base is already the newest version (16-20260322-1). libdb5.3t64 is already the newest version (5.3.28+dfsg2-11+b1). gcc is already the newest version (4:15.2.0-5). gcc 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. diffutils is already the newest version (1:3.12-1). libstdc++-15-dev is already the newest version (15.2.0-16). libstdc++-15-dev set to manually installed. libmagic-mgc is already the newest version (1:5.46-5+b1). libmagic-mgc set to manually installed. m4 is already the newest version (1.4.21-1). m4 set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.2-3). libopenmpi-dev is already the newest version (5.0.10-1). libopenmpi-dev set to manually installed. libnuma-dev is already the newest version (2.0.19-1+b1). libnuma-dev set to manually installed. libsframe3 is already the newest version (2.46-3). libsframe3 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. libsprng2-dev is already the newest version (2.0a-19). libsprng2-dev set to manually installed. libc6 is already the newest version (2.42-14). libdrm-amdgpu1 is already the newest version (2.4.131-1). libdrm-amdgpu1 set to manually installed. dpkg is already the newest version (1.23.7). 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. libdpkg-perl is already the newest version (1.23.7). libdpkg-perl set to manually installed. libnettle8t64 is already the newest version (3.10.2-1+b1). libnettle8t64 set to manually installed. grep is already the newest version (3.12-1). libquadmath0 is already the newest version (16-20260322-1). libquadmath0 set to manually installed. libgcc-15-dev is already the newest version (15.2.0-16). libgcc-15-dev set to manually installed. libpkgconf7 is already the newest version (2.5.1-4). libpkgconf7 set to manually installed. gcc-15-x86-64-linux-gnu is already the newest version (15.2.0-16). gcc-15-x86-64-linux-gnu set to manually installed. sensible-utils is already the newest version (0.0.26). sensible-utils 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. dash is already the newest version (0.5.12-12). librhash1 is already the newest version (1.4.6-1.1). librhash1 set to manually installed. libnl-3-dev is already the newest version (3.12.0-2). libnl-3-dev set to manually installed. googletest is already the newest version (1.17.0-1). googletest set to manually installed. libldap2 is already the newest version (2.6.10+dfsg-1+b1). libldap2 set to manually installed. libxcb1 is already the newest version (1.17.0-2+b2). libxcb1 set to manually installed. mpi-default-dev is already the newest version (1.20). mpi-default-dev set to manually installed. libboost1.90-dev is already the newest version (1.90.0-6). libboost1.90-dev set to manually installed. libisl23 is already the newest version (0.27-2). libisl23 set to manually installed. libcap-ng0 is already the newest version (0.9.2-1). base-passwd is already the newest version (3.6.8). libxext6 is already the newest version (2:1.3.4-1+b4). libxext6 set to manually installed. libssh2-1t64 is already the newest version (1.11.1-2). libssh2-1t64 set to manually installed. libgmpxx4ldbl is already the newest version (2:6.3.0+dfsg-5+b1). libgmpxx4ldbl set to manually installed. libucx0 is already the newest version (1.20.1~rc2-1). libucx0 set to manually installed. libssl3t64 is already the newest version (3.6.2-1). libunistring5 is already the newest version (1.4.2-1). libunistring5 set to manually installed. libngtcp2-crypto-ossl0 is already the newest version (1.21.0-1). libngtcp2-crypto-ossl0 set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libedit2 is already the newest version (3.1-20251016-1). libedit2 set to manually installed. perl-base is already the newest version (5.40.1-7+b1). openssl-provider-legacy is already the newest version (3.6.2-1). automake is already the newest version (1:1.18.1-4). automake set to manually installed. dh-autoreconf is already the newest version (22). dh-autoreconf set to manually installed. libaudit-common is already the newest version (1:4.1.2-1). libsystemd0 is already the newest version (260.1-1). libfabric1 is already the newest version (2.1.0-1.1+b1). libfabric1 set to manually installed. libdrm-common is already the newest version (2.4.131-1). libdrm-common set to manually installed. systemd is already the newest version (260.1-1). systemd set to manually installed. libhwloc-plugins is already the newest version (2.13.0-2). libhwloc-plugins set to manually installed. g++-15 is already the newest version (15.2.0-16). g++-15 set to manually installed. libhwasan0 is already the newest version (16-20260322-1). libhwasan0 set to manually installed. intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian 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. libperl5.40 is already the newest version (5.40.1-7+b1). libperl5.40 set to manually installed. man-db is already the newest version (2.13.1-1). man-db set to manually installed. file is already the newest version (1:5.46-5+b1). file set to manually installed. libpsm2-2 is already the newest version (11.2.185-2.1). libpsm2-2 set to manually installed. libfuse3-4 is already the newest version (3.18.2-1). libfuse3-4 set to manually installed. make is already the newest version (4.4.1-3). make set to manually installed. libsasl2-2 is already the newest version (2.1.28+dfsg1-11). libsasl2-2 set to manually installed. libxdmcp6 is already the newest version (1:1.1.5-2). libxdmcp6 set to manually installed. libgomp1 is already the newest version (16-20260322-1). libgomp1 set to manually installed. libkrb5support0 is already the newest version (1.22.1-2+b1). libkrb5support0 set to manually installed. libgmp10 is already the newest version (2:6.3.0+dfsg-5+b1). groff-base is already the newest version (1.23.0-10). groff-base set to manually installed. gfortran-15 is already the newest version (15.2.0-16). gfortran-15 set to manually installed. libprrte-bin is already the newest version (3.0.13-3). libprrte-bin set to manually installed. libarchive13t64 is already the newest version (3.8.5-1). libarchive13t64 set to manually installed. libkrb5-3 is already the newest version (1.22.1-2+b1). libkrb5-3 set to manually installed. libcom-err2 is already the newest version (1.47.4-1). libcom-err2 set to manually installed. ncurses-bin is already the newest version (6.6+20251231-1). autotools-dev is already the newest version (20240727.1). autotools-dev set to manually installed. liblsan0 is already the newest version (16-20260322-1). liblsan0 set to manually installed. help2man is already the newest version (1.49.3). help2man set to manually installed. tar is already the newest version (1.35+dfsg-4). libnl-route-3-dev is already the newest version (3.12.0-2). libnl-route-3-dev set to manually installed. libdebhelper-perl is already the newest version (13.31). libdebhelper-perl set to manually installed. libnghttp2-14 is already the newest version (1.68.1-1). libnghttp2-14 set to manually installed. libpsl5t64 is already the newest version (0.21.5-1). libpsl5t64 set to manually installed. libc-gconv-modules-extra is already the newest version (2.42-14). libibverbs1 is already the newest version (61.0-2). libibverbs1 set to manually installed. libze1 is already the newest version (1.28.2-2). libze1 set to manually installed. libsprng2 is already the newest version (2.0a-19). libsprng2 set to manually installed. libgcc-s1 is already the newest version (16-20260322-1). libgdbm6t64 is already the newest version (1.26-1+b1). libgdbm6t64 set to manually installed. libngtcp2-16 is already the newest version (1.21.0-1). libngtcp2-16 set to manually installed. binutils is already the newest version (2.46-3). binutils set to manually installed. hostname is already the newest version (3.25). dwz is already the newest version (0.16-4). dwz set to manually installed. passwd is already the newest version (1:4.19.3-2). passwd set to manually installed. autopoint is already the newest version (0.23.2-2). autopoint set to manually installed. build-essential is already the newest version (12.12). build-essential set to manually installed. g++ is already the newest version (4:15.2.0-5). g++ set to manually installed. libitm1 is already the newest version (16-20260322-1). libitm1 set to manually installed. pkgconf is already the newest version (2.5.1-4). pkgconf set to manually installed. libctf-nobfd0 is already the newest version (2.46-3). libctf-nobfd0 set to manually installed. libdrm2 is already the newest version (2.4.131-1). libdrm2 set to manually installed. libmd0 is already the newest version (1.1.0-2+b2). libbsd0 is already the newest version (0.12.2-2+b1). libbsd0 set to manually installed. libnl-3-200 is already the newest version (3.12.0-2). libnl-3-200 set to manually installed. libubsan1 is already the newest version (16-20260322-1). libubsan1 set to manually installed. libxau6 is already the newest version (1:1.0.11-1+b1). libxau6 set to manually installed. po-debconf is already the newest version (1.0.22). po-debconf set to manually installed. libevent-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-2.1-7t64 set to manually installed. gcc-15 is already the newest version (15.2.0-16). gcc-15 set to manually installed. openssh-client is already the newest version (1:10.3p1-1). openssh-client 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. libmpfr6 is already the newest version (4.2.2-3). libmpfr6 set to manually installed. util-linux is already the newest version (2.42-3). sed is already the newest version (4.9-2). adduser is already the newest version (3.155). adduser set to manually installed. libudev1 is already the newest version (260.1-1). libx11-6 is already the newest version (2:1.8.13-1). libx11-6 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. libamdhip64-6 is already the newest version (6.4.3-5). libamdhip64-6 set to manually installed. libffi8 is already the newest version (3.5.2-4). libffi8 set to manually installed. libucc1 is already the newest version (1.7.0~rc1-1). libucc1 set to manually installed. libaudit1 is already the newest version (1:4.1.2-1+b1). libcbor0.10 is already the newest version (0.10.2-2.1). libcbor0.10 set to manually installed. openmpi-common is already the newest version (5.0.10-1). openmpi-common set to manually installed. libk5crypto3 is already the newest version (1.22.1-2+b1). libk5crypto3 set to manually installed. rpcsvc-proto is already the newest version (1.4.3-1). rpcsvc-proto set to manually installed. sysvinit-utils is already the newest version (3.18-1). libgmp-dev is already the newest version (2:6.3.0+dfsg-5+b1). libgmp-dev set to manually installed. libgfortran-15-dev is already the newest version (15.2.0-16). libgfortran-15-dev 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. libdebconfclient0 is already the newest version (0.282+b2). libpcre2-8-0 is already the newest version (10.46-1+b1). libsasl2-modules-db is already the newest version (2.1.28+dfsg1-11). libsasl2-modules-db set to manually installed. libsystemd-shared is already the newest version (260.1-1). libsystemd-shared set to manually installed. libbz2-1.0 is already the newest version (1.0.8-6+b1). libsimde-dev is already the newest version (0.8.4~rc3-5). libsimde-dev set to manually installed. libzstd1 is already the newest version (1.5.7+dfsg-3+b1). ocl-icd-libopencl1 is already the newest version (2.3.4-1). ocl-icd-libopencl1 set to manually installed. 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. libibverbs-dev is already the newest version (61.0-2). libibverbs-dev set to manually installed. libhwloc-dev is already the newest version (2.13.0-2). libhwloc-dev set to manually installed. libevent-pthreads-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-pthreads-2.1-7t64 set to manually installed. libbrotli1 is already the newest version (1.2.0-3). libbrotli1 set to manually installed. base-files is already the newest version (14). debconf is already the newest version (1.5.92). libexpat1 is already the newest version (2.7.5-1). libexpat1 set to manually installed. libfile-stripnondeterminism-perl is already the newest version (1.15.0-1). libfile-stripnondeterminism-perl 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. libhsa-runtime64-1 is already the newest version (6.4.3+dfsg-5). libhsa-runtime64-1 set to manually installed. libctf0 is already the newest version (2.46-3). libctf0 set to manually installed. libpam0g is already the newest version (1.7.0-5+b1). libx11-data is already the newest version (2:1.8.13-1). libx11-data set to manually installed. login.defs is already the newest version (1:4.19.3-2). login.defs set to manually installed. libopenmpi40 is already the newest version (5.0.10-1). libopenmpi40 set to manually installed. libpam-runtime is already the newest version (1.7.0-5). libprrte3 is already the newest version (3.0.13-3). libprrte3 set to manually installed. libsemanage-common is already the newest version (3.10-1). libsemanage-common set to manually installed. mawk is already the newest version (1.3.4.20260302-1). librdmacm1t64 is already the newest version (61.0-2). librdmacm1t64 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. libpipeline1 is already the newest version (1.5.8-2+b1). libpipeline1 set to manually installed. cmake is already the newest version (4.3.1-1). cmake set to manually installed. libyaml-cpp-dev is already the newest version (0.8.0+dfsg-9). libyaml-cpp-dev set to manually installed. libcc1-0 is already the newest version (16-20260322-1). libcc1-0 set to manually installed. libselinux1 is already the newest version (3.10-1). procps is already the newest version (2:4.0.4-9+b1). procps set to manually installed. libtool is already the newest version (2.5.4-11). libtool set to manually installed. libhwloc15 is already the newest version (2.13.0-2). libhwloc15 set to manually installed. gzip is already the newest version (1.13-1). libproc2-0 is already the newest version (2:4.0.4-9+b1). libproc2-0 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. ibverbs-providers is already the newest version (61.0-2). ibverbs-providers set to manually installed. libeigen3-dev is already the newest version (3.4.0-5). libeigen3-dev set to manually installed. libmagic1t64 is already the newest version (1:5.46-5+b1). libmagic1t64 set to manually installed. libmunge2 is already the newest version (0.5.18-1). libmunge2 set to manually installed. libattr1 is already the newest version (1:2.5.2-4). libibmad5 is already the newest version (61.0-2). libibmad5 set to manually installed. gettext-base is already the newest version (0.23.2-2). gettext-base set to manually installed. libncursesw6 is already the newest version (6.6+20251231-1). libncursesw6 set to manually installed. findutils is already the newest version (4.10.0-3). libpmix2t64 is already the newest version (6.0.0+really5.0.9-3). libpmix2t64 set to manually installed. libsemanage2 is already the newest version (3.10-1). libsemanage2 set to manually installed. perl is already the newest version (5.40.1-7+b1). perl 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. coreutils is already the newest version (9.10-1). libfido2-1 is already the newest version (1.17.0-1). libfido2-1 set to manually installed. liblz4-1 is already the newest version (1.10.0-9). liblz4-1 set to manually installed. The following NEW packages will be installed: pkg-config 127.0.0.1 - - [20/Apr/2026 19:44:51] "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:34481 ./ pkg-config 2.5.1-4 [18.1 kB] Fetched 18.1 kB in 0s (0 B/s) Chrooting into /srv/rebuilderd/tmp/mmdebstrap.5uCs7jIffE/ 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 ... 41931 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.5uCs7jIffE/ 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.5uCs7jIffE (Reading database ... 41936 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.5uCs7jIffE I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.5uCs7jIffE 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.5uCs7jIffE... I: success in 99.9306 seconds Downloading dependency 261 of 270: gettext-base:amd64=0.23.2-2 Downloading dependency 262 of 270: libncursesw6:amd64=6.6+20251231-1 Downloading dependency 263 of 270: findutils:amd64=4.10.0-3 Downloading dependency 264 of 270: libpmix2t64:amd64=6.0.0+really5.0.9-3 Downloading dependency 265 of 270: libsemanage2:amd64=3.10-1 Downloading dependency 266 of 270: perl:amd64=5.40.1-7+b1 Downloading dependency 267 of 270: cpp-x86-64-linux-gnu:amd64=4:15.2.0-5 Downloading dependency 268 of 270: coreutils:amd64=9.10-1 Downloading dependency 269 of 270: libfido2-1:amd64=1.17.0-1 Downloading dependency 270 of 270: liblz4-1:amd64=1.10.0-9 env --chdir=/srv/rebuilderd/tmp/rebuilderdxJKJah/out DEB_BUILD_OPTIONS=parallel=6 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1776414804 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildSfAXXf/debrebuild.sbuildrc.J4fAHnsjsOUF sbuild --build=amd64 --host=amd64 --arch-any --no-arch-all --chroot=/srv/rebuilderd/tmp/debrebuildSfAXXf/debrebuild.tar.6hhcDzCQDnSL --chroot-mode=unshare --dist=unstable --no-run-lintian --no-run-piuparts --no-run-autopkgtest --no-apt-update --no-apt-upgrade --no-apt-distupgrade --no-source --verbose --nolog --bd-uninstallable-explainer= --build-path=/build/reproducible-path --dsc-dir=iqtree3-3.1.1+dfsg /srv/rebuilderd/tmp/rebuilderdxJKJah/inputs/iqtree3_3.1.1+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 +==============================================================================+ | iqtree3 3.1.1+dfsg-1 (amd64) Mon, 20 Apr 2026 19:44:59 +0000 | +==============================================================================+ Package: iqtree3 Version: 3.1.1+dfsg-1 Source Version: 3.1.1+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/debrebuildSfAXXf/debrebuild.tar.6hhcDzCQDnSL to /srv/rebuilderd/tmp/tmp.sbuild.vbLvWn48OE... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Mon, 20 Apr 2026 19:45:05 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdxJKJah/inputs/iqtree3_3.1.1+dfsg-1.dsc exists in /srv/rebuilderd/tmp/rebuilderdxJKJah/inputs; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 20 Apr 2026 19:45:06 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), cmake, googletest, libboost-dev, libeigen3-dev, libncl-dev, libsimde-dev, libsprng2-dev, libyaml-cpp-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath, build-essential Filtered Build-Depends: debhelper-compat (= 13), cmake, googletest, libboost-dev, libeigen3-dev, libncl-dev, libsimde-dev, libsprng2-dev, libyaml-cpp-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-CpJ1QL/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Mon, 20 Apr 2026 19:45:09 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 arm64) +------------------------------------------------------------------------------+ | Build environment Mon, 20 Apr 2026 19:45:09 +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_6.19.12-1 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_1.90.0.2 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+b1 libctf-nobfd0_2.46-3 libctf0_2.46-3 libcurl4t64_8.20.0~rc2-1 libdb5.3t64_5.3.28+dfsg2-11+b1 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_1.17.0-1 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 libgomp1_16-20260322-1 libgprofng0_2.46-3 libgssapi-krb5-2_1.22.1-2+b1 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_2.5.4-11 libltdl7_2.5.4-11 liblz4-1_1.10.0-9 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 libncl-dev_2.1.21+git20210811.b1213a7-6+b1 libncl2_2.1.21+git20210811.b1213a7-6+b1 libncursesw6_6.6+20251231-1 libnettle8t64_3.10.2-1+b1 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 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+b1 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 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_3.6.2-1 libstdc++-15-dev_15.2.0-16 libstdc++6_16-20260322-1 libsystemd-shared_260.1-1 libsystemd0_260.1-1 libtinfo6_6.6+20251231-1 libtool_2.5.4-11 libtsan2_16-20260322-1 libubsan1_16-20260322-1 libucc1_1.7.0~rc1-1 libuchardet0_0.0.8-2+b1 libucx0_1.20.1~rc2-1 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_6.19.12-1 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_1:10.3p1-1 openssl-provider-legacy_3.6.2-1 passwd_1:4.19.3-2 patch_2.8-2 perl_5.40.1-7+b1 perl-base_5.40.1-7+b1 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 Mon, 20 Apr 2026 19:45:09 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: iqtree3 Binary: iqtree3 Architecture: amd64 arm64 Version: 3.1.1+dfsg-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/iqtree3 Vcs-Git: https://salsa.debian.org/med-team/iqtree3.git Testsuite: autopkgtest Testsuite-Triggers: time Build-Depends: debhelper-compat (= 13), cmake, googletest, libboost-dev, libeigen3-dev, libncl-dev, libsimde-dev, libsprng2-dev, libyaml-cpp-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath Package-List: iqtree3 deb science optional arch=amd64,arm64 Checksums-Sha1: 5cb91218fe0eb28acb346c2314a279e169827bc1 2314716 iqtree3_3.1.1+dfsg.orig.tar.xz 78f51f157913f08d5eb69c81ec304756f360bb5a 23900 iqtree3_3.1.1+dfsg-1.debian.tar.xz Checksums-Sha256: abafa0ab7d5b33a214831dbb7e5e7c80b67572b57787f34b961617d4e79d30f3 2314716 iqtree3_3.1.1+dfsg.orig.tar.xz 033c60708e37fa4c575779fa2b2a2f03320f62c7a13fda2f4702769b75cd7c6b 23900 iqtree3_3.1.1+dfsg-1.debian.tar.xz Files: 8c195f00eb541abb6392e19f0d445e4f 2314716 iqtree3_3.1.1+dfsg.orig.tar.xz 33d32738a82f3dcd102bf9940e15921d 23900 iqtree3_3.1.1+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmniDqASHGNydXNvZUBk ZWJpYW4ub3JnAAoJEDwmdj9sZ+bi0oQQAL6k1bFVEOxxP3lfg1stzHI4UDsMa6D4 hJqzA+FnMrBACoXHKK3I+b0spuDQVdru0bqkADvhjMLgDA2IxDYy1KTxFu2psTxy /hg3/TZXzk73LhclE/+FZf3xBIEpprwKZR4devs6Ma/xflbykmyoHRjIEMjEsn/s mvBqqbXpemOJ2p1neStFHGLaXuQ0hHbQZfBqQDIG+x23de2Omn5ZTWerlBy1VGHP hSTRKyyj+pqzhGDe3RUquY8td7u31yQAkCCNXWupqLJoCVqxDHHwdg9MJW5/shkR jE2Syk2Y4mfQUyda3lOQppr04PkotXUls65r0z5LtYSr4UDcVgHM6xhkzjWy/Oja OjWBAoY7We9uTXGL52vDi8wvYfaHl6yNAuwx0JVTRFT8jsusQaK2qjmkRtQxAeeq OSukhuBO8Bo1MqPIcwgCH6PHIP/3WGSmgP/tj5rm1Ucfr0iEYQ51nRx17dZ3ZDWk jcvG1/LpVHXOO4uIz9QhD1Ro59uOfxVa2py86kkIYvPU4eUwwWYLwJ8dBdVeMfwo O5eUDuXGk7hQmc5FOmtUQlAAovdPj0x6DqERhGvTdI1q5BcuotYKlGCi1AxhvnXb 8GwrrTA699gtkc0ThZXR+uitwCzHYswklARgcmUirZi8XMQD0NZI97d3HNyT0FZz wKtw07a67Uad =RSE2 -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./iqtree3_3.1.1+dfsg-1.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./iqtree3_3.1.1+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 iqtree3 in /build/reproducible-path/iqtree3-3.1.1+dfsg dpkg-source: info: unpacking iqtree3_3.1.1+dfsg.orig.tar.xz dpkg-source: info: unpacking iqtree3_3.1.1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying cmake-4.patch dpkg-source: info: applying packaged-libs dpkg-source: info: applying no-baseline-violations 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=1776414804 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -B dpkg-buildpackage: info: source package iqtree3 dpkg-buildpackage: info: source version 3.1.1+dfsg-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/iqtree3-3.1.1+dfsg' dh_auto_clean -Bbuild.omp dh_auto_clean -Bbuild.serial dh_auto_clean -Bbuild.mpi dh override_dh_auto_clean make[1]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' dh_auto_configure -Bbuild.omp -- -DIQTREE_FLAGS="omp" cd build.omp && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/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:99 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.90.0/BoostConfig.cmake (found version "1.90.0") -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include IQ-TREE flags : omp Build lib : OFF Integrate CMAPLE: ON Integrate CMAPLE_AA: OFF Build IQTREE library: OFF Target OS : Unix Compiler : GNU Compiler (gcc) Compiler version: 15.2.0 Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.2") Using system zlib CMake Deprecation Warning at cmaple/CMakeLists.txt:55 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. No clang-tidy (USE_CLANG_TIDY=OFF) Target OS : Unix OpenMP : Yes LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--gc-sections Using system zlib -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- clang-tidy not found. -- Configuring done (1.3s) -- 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/iqtree3-3.1.1+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:99 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.90.0/BoostConfig.cmake (found version "1.90.0") -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include IQ-TREE flags : Build lib : OFF Integrate CMAPLE: ON Integrate CMAPLE_AA: OFF Build IQTREE library: OFF Target OS : Unix Compiler : GNU Compiler (gcc) Compiler version: 15.2.0 Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.2") Using system zlib CMake Deprecation Warning at cmaple/CMakeLists.txt:55 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. No clang-tidy (USE_CLANG_TIDY=OFF) Target OS : Unix OpenMP : Yes LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--gc-sections Using system zlib -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- clang-tidy not found. -- Configuring done (1.3s) -- 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/iqtree3-3.1.1+dfsg/build.serial dh_auto_configure -Bbuild.mpi -- -DIQTREE_FLAGS="mpi" cd build.mpi && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/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:99 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.90.0/BoostConfig.cmake (found version "1.90.0") -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include IQ-TREE flags : mpi Build lib : OFF Integrate CMAPLE: ON Integrate CMAPLE_AA: OFF Build IQTREE library: OFF Target OS : Unix Compiler : GNU Compiler (gcc) Compiler version: 15.2.0 Target binary : 64-bit -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") OpenMP : Yes MPI : Yes Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.2") Using system zlib CMake Deprecation Warning at cmaple/CMakeLists.txt:55 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. No clang-tidy (USE_CLANG_TIDY=OFF) Target OS : Unix OpenMP : Yes LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--gc-sections Using system zlib -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- clang-tidy not found. -- Configuring done (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/iqtree3-3.1.1+dfsg/build.mpi dh override_dh_auto_configure make[1]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' dh_auto_build -Bbuild.omp cd build.omp && make -j6 INSTALL="install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' /usr/bin/cmake -S/build/reproducible-path/iqtree3-3.1.1+dfsg -B/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/CMakeFiles /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/depend make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" kernelsse make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" kernelavx make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" kernelfma make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2 /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lsd2 /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lsd2/CMakeFiles/lsd2.dir/DependInfo.cmake "--color=" lsd2 make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/booster /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" booster make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" pll make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylokernelsse.cpp [ 1%] 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_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylokernelfma.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 2%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o [ 2%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -MF CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o.d -o CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/confidence_interval.cpp /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylotreeavx.cpp [ 2%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/bitset_index.c [ 3%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/alignment.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 3%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c [ 3%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/hashmap.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c:43: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c:326:3: note: in expansion of macro ‘rax_posix_memalign’ 326 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 3%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluateGenericSpecial.c [ 4%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/io.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluateGenericSpecial.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 4%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/sort.c [ 4%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/tree.c [ 5%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/booster.c [ 5%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/hashtables_bfields.c [ 6%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:1173:3: note: in expansion of macro ‘rax_posix_memalign’ 1173 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:1015:3: note: in expansion of macro ‘rax_posix_memalign’ 1015 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:1324:3: note: in expansion of macro ‘rax_posix_memalign’ 1324 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:934:3: note: in expansion of macro ‘rax_posix_memalign’ 934 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 6%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/prng.c [ 7%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/stats.c [ 7%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:115: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:1701:7: note: in expansion of macro ‘rax_posix_memalign’ 1701 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:1777:3: note: in expansion of macro ‘rax_posix_memalign’ 1777 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/tree_utils.c [ 7%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 7%] Built target booster make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" ncl make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 8%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsassumptionsblock.cpp [ 8%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/hardware.c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/hardware.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/hash.c [ 9%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/lexer.c [ 9%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:41: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:2686:3: note: in expansion of macro ‘rax_posix_memalign’ 2686 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:3061:3: note: in expansion of macro ‘rax_posix_memalign’ 3061 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/models.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/models.c:47: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsblock.cpp [ 10%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o -MF CMakeFiles/lsd2.dir/src/dating.cpp.o.d -o CMakeFiles/lsd2.dir/src/dating.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/dating.cpp [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxscharactersblock.cpp [ 10%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newick.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 10%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:46: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:2766:13: note: in expansion of macro ‘rax_posix_memalign’ 2766 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:2795:17: note: in expansion of macro ‘rax_posix_memalign’ 2795 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:3733:11: note: in expansion of macro ‘rax_posix_memalign’ 3733 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:3803:3: note: in expansion of macro ‘rax_posix_memalign’ 3803 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -MF CMakeFiles/lsd2.dir/src/estimate_root.cpp.o.d -o CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/estimate_root.cpp [ 11%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/genericParallelization.c [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsdatablock.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 12%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/optimizeModel.c [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsdiscretedatum.cpp [ 13%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o -MF CMakeFiles/lsd2.dir/src/lsd.cpp.o.d -o CMakeFiles/lsd2.dir/src/lsd.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/lsd.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/optimizeModel.c:44: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsdiscretematrix.cpp [ 13%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/parsePartition.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 14%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/queue.c [ 14%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/randomTree.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 14%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/recom.c:41: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 14%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o -MF CMakeFiles/lsd2.dir/src/options.cpp.o.d -o CMakeFiles/lsd2.dir/src/options.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp [ 15%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/restartHashTable.c [ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsdistancedatum.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/restartHashTable.c:41: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/searchAlgo.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/searchAlgo.c:45: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsdistancesblock.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp: In function ‘Pr* getInterface()’: /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:306:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 306 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:311:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 311 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:338:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 338 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:342:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp: In function ‘void setOptionsWithLetter(Pr*, char)’: /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:872:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 872 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:877:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:923:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 923 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/ssort.c [ 17%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/stack.c [ 17%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/topologies.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/topologies.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsemptyblock.cpp [ 17%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/trash.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/treeIO.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/treeIO.c:41: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:67: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:44: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:596:7: note: in expansion of macro ‘rax_posix_memalign’ 596 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:597:7: note: in expansion of macro ‘rax_posix_memalign’ 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:599:7: note: in expansion of macro ‘rax_posix_memalign’ 599 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:605:7: note: in expansion of macro ‘rax_posix_memalign’ 605 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:617:15: note: in expansion of macro ‘rax_posix_memalign’ 617 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:621:15: note: in expansion of macro ‘rax_posix_memalign’ 621 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:687:7: note: in expansion of macro ‘rax_posix_memalign’ 687 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:694:7: note: in expansion of macro ‘rax_posix_memalign’ 694 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:724:7: note: in expansion of macro ‘rax_posix_memalign’ 724 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:744:7: note: in expansion of macro ‘rax_posix_memalign’ 744 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:756:11: note: in expansion of macro ‘rax_posix_memalign’ 756 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsexception.cpp [ 20%] Linking C static library libpll.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 20%] Built target pll [ 20%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o -MF CMakeFiles/lsd2.dir/src/outliers.cpp.o.d -o CMakeFiles/lsd2.dir/src/outliers.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/outliers.cpp [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsreader.cpp [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxssetreader.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsstring.cpp make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/nclextra /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" nclextra make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 21%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra/mpdablock.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxstaxablock.cpp [ 22%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o -MF CMakeFiles/lsd2.dir/src/readData.cpp.o.d -o CMakeFiles/lsd2.dir/src/readData.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/readData.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxstoken.cpp [ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra/msetsblock.cpp [ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxstreesblock.cpp [ 24%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 [ 24%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o -MF CMakeFiles/lsd2.dir/src/utils.cpp.o.d -o CMakeFiles/lsd2.dir/src/utils.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/utils.cpp /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/iqtree3-3.1.1+dfsg/build.omp' [ 24%] Built target ncl make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/sprng /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" sprng make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 24%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/lcg64.c [ 24%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/makeseed.c [ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra/msplitsblock.cpp [ 24%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/memory.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/store.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/primes-lcg64.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/checkid.c [ 26%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 26%] Built target sprng make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/lbfgsb /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lbfgsb /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" lbfgsb make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 26%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lbfgsb/lbfgsb_new.cpp [ 26%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 26%] Built target lbfgsb make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/whtest /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" whtest make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 26%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/eigen.c [ 26%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra/modelsblock.cpp [ 26%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/eigen_sym.c [ 27%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/random.c [ 27%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/weisslambda.c [ 27%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/weisslambda_sub.c [ 28%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest.c [ 29%] Linking CXX static library libnclextra.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 29%] Built target nclextra make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/vectorclass /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/vectorclass /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" vectorclass make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 29%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/vectorclass/instrset_detect.cpp [ 29%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c [ 30%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 30%] Built target vectorclass make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/gsl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" gsl make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 30%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/binomial_tpe.cpp [ 30%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/multinomial.cpp [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/pow_int.cpp [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/gauss.cpp [ 31%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_wrapper.cpp [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/gaussinv.cpp [ 32%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/gausspdf.cpp [ 32%] Linking CXX static library libgsl.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake [ 32%] Linking CXX static library liblsd2.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lsd2 && /usr/bin/cmake -P CMakeFiles/lsd2.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/lsd2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/lsd2.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 32%] Built target gsl make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/utils/CMakeFiles/cmaple_utils.dir/DependInfo.cmake "--color=" cmaple_utils make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 33%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/utils && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o -MF CMakeFiles/cmaple_utils.dir/tools.cpp.o.d -o CMakeFiles/cmaple_utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/tools.cpp /usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 33%] Built target lsd2 make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" pllavx make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 34%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/avxLikelihood.c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/tools.cpp:44:23: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 44 | out << " built " << __DATE__ << std::endl; | ^~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/avxLikelihood.c:60: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 35%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 35%] Built target whtest make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/phylo-yaml /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/phylo-yaml /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" phyloYAML make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 35%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/phylo-yaml/statespace.cpp [ 35%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/utils && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -MF CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/operatingsystem.cpp [ 35%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 35%] Built target pllavx make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" terraphast make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 35%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/advanced.cpp [ 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/iqtree3-3.1.1+dfsg/build.omp' [ 35%] Built target kernelsse [ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/bigint.cpp [ 36%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/utils && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/gzstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/gzstream.cpp make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/utils/CMakeFiles/decentTree.dir/DependInfo.cmake "--color=" decentTree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 36%] Building CXX object utils/CMakeFiles/decentTree.dir/decenttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/decenttree.cpp.o -MF CMakeFiles/decentTree.dir/decenttree.cpp.o.d -o CMakeFiles/decentTree.dir/decenttree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/decenttree.cpp [ 37%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/logstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/logstream.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/logstream.cpp [ 38%] Building CXX object utils/CMakeFiles/decentTree.dir/starttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/starttree.cpp.o -MF CMakeFiles/decentTree.dir/starttree.cpp.o.d -o CMakeFiles/decentTree.dir/starttree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/starttree.cpp [ 38%] Linking CXX static library libcmaple_utils.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/utils && /usr/bin/cmake -P CMakeFiles/cmaple_utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_utils.dir/link.txt --verbose=1 "/usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 38%] Built target cmaple_utils make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" utils make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 40%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/eigendecomposition.cpp [ 40%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj.cpp.o -MF CMakeFiles/decentTree.dir/bionj.cpp.o.d -o CMakeFiles/decentTree.dir/bionj.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/bionj.cpp [ 40%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/bipartitions.cpp [ 40%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj2.cpp.o -MF CMakeFiles/decentTree.dir/bionj2.cpp.o.d -o CMakeFiles/decentTree.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/bionj2.cpp [ 40%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/bitmatrix.cpp [ 40%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/gzstream.cpp [ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/clamped_uint.cpp [ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/constraints.cpp [ 41%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/optimization.cpp [ 41%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 41%] Built target phyloYAML make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pda /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pda /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" pda make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 41%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/circularnetwork.cpp [ 42%] 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/iqtree3-3.1.1+dfsg/build.omp' [ 42%] Built target kernelavx make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/alignment/CMakeFiles/cmaple_alignment.dir/DependInfo.cmake "--color=" cmaple_alignment make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 42%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/alignment && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -MF CMakeFiles/cmaple_alignment.dir/mutation.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/mutation.cpp [ 43%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/stoprule.cpp [ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/errors.cpp [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/multitree.cpp [ 45%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/alignment && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregion.cpp [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/multitree_iterator.cpp [ 45%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/greedy.cpp [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/nodes.cpp [ 46%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/parser.cpp [ 46%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/alignment && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.cpp [ 46%] 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/iqtree3-3.1.1+dfsg/build.omp' [ 46%] Built target kernelfma [ 47%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/gurobiwrapper.cpp [ 47%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/alignment && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.cpp [ 47%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/tools.cpp [ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/rooting.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 47%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/pllnni.cpp [ 48%] Building CXX object utils/CMakeFiles/decentTree.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/gzstream.cpp.o -MF CMakeFiles/decentTree.dir/gzstream.cpp.o.d -o CMakeFiles/decentTree.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/gzstream.cpp [ 48%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/hashsplitset.cpp [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/simple.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.h:3, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 48%] Building CXX object utils/CMakeFiles/decentTree.dir/progress.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/progress.cpp.o -MF CMakeFiles/decentTree.dir/progress.cpp.o.d -o CMakeFiles/decentTree.dir/progress.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/progress.cpp [ 49%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -MF CMakeFiles/cmaple_alignment.dir/sequence.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/subtree_extraction.cpp [ 50%] Building CXX object utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o -MF CMakeFiles/decentTree.dir/operatingsystem.cpp.o.d -o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/operatingsystem.cpp [ 50%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/pdnetwork.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 51%] Linking CXX executable decentTree cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/decentTree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/decentTree.dir/link.d CMakeFiles/decentTree.dir/decenttree.cpp.o CMakeFiles/decentTree.dir/starttree.cpp.o CMakeFiles/decentTree.dir/bionj.cpp.o CMakeFiles/decentTree.dir/bionj2.cpp.o CMakeFiles/decentTree.dir/gzstream.cpp.o CMakeFiles/decentTree.dir/progress.cpp.o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -o decentTree -L/build/reproducible-path/iqtree3-3.1.1+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+dfsg/lib /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 51%] Built target decentTree [ 52%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/checkpoint.cpp [ 52%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -MF CMakeFiles/cmaple_alignment.dir/alignment.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.cpp [ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/supertree_helpers.cpp [ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/trees.cpp [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/union_find.cpp [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/validation.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 53%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/MPIHelper.cpp [ 53%] Linking CXX static library libcmaple_alignment.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/alignment && /usr/bin/cmake -P CMakeFiles/cmaple_alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_alignment.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-15" qc libcmaple_alignment.a CMakeFiles/cmaple_alignment.dir/mutation.cpp.o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o "/usr/bin/gcc-ranlib-15" libcmaple_alignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 53%] Built target cmaple_alignment [ 53%] Building CXX object utils/CMakeFiles/utils.dir/starttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/starttree.cpp.o -MF CMakeFiles/utils.dir/starttree.cpp.o.d -o CMakeFiles/utils.dir/starttree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/starttree.cpp [ 53%] Linking CXX static library libterraphast.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 [ 54%] Building CXX object utils/CMakeFiles/utils.dir/bionj.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj.cpp.o -MF CMakeFiles/utils.dir/bionj.cpp.o.d -o CMakeFiles/utils.dir/bionj.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/bionj.cpp /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/iqtree3-3.1.1+dfsg/build.omp' [ 54%] Built target terraphast [ 55%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/pruning.cpp [ 55%] Building CXX object utils/CMakeFiles/utils.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj2.cpp.o -MF CMakeFiles/utils.dir/bionj2.cpp.o.d -o CMakeFiles/utils.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/bionj2.cpp [ 55%] Building CXX object utils/CMakeFiles/utils.dir/progress.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/progress.cpp.o -MF CMakeFiles/utils.dir/progress.cpp.o.d -o CMakeFiles/utils.dir/progress.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/progress.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/operatingsystem.cpp.o -MF CMakeFiles/utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/operatingsystem.cpp make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/model/CMakeFiles/cmaple_model.dir/DependInfo.cmake "--color=" cmaple_model make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 56%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/model && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o -MF CMakeFiles/cmaple_model.dir/model.cpp.o.d -o CMakeFiles/cmaple_model.dir/model.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/split.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/splitgraph.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/splitset.cpp [ 57%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/lpwrapper.c [ 57%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/ecopd.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 57%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o -MF CMakeFiles/cmaple_model.dir/modelbase.cpp.o.d -o CMakeFiles/cmaple_model.dir/modelbase.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/modelbase.cpp [ 58%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/model && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o -MF CMakeFiles/cmaple_model.dir/model_dna.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_dna.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/modelbase.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 58%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/graph.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 60%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/pdtree.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/pdtreeset.cpp [ 60%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/model && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o -MF CMakeFiles/cmaple_model.dir/model_aa.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_aa.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/ecopdmtreeset.cpp [ 60%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 60%] Built target utils [ 60%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/model && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o -MF CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:34: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:319:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 319 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" model make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 60%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelmarkov.cpp [ 60%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelbin.cpp [ 61%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modeldna.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.h:3, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 61%] Building CXX object model/CMakeFiles/model.dir/modeldnaerror.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldnaerror.cpp.o -MF CMakeFiles/model.dir/modeldnaerror.cpp.o.d -o CMakeFiles/model.dir/modeldnaerror.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modeldnaerror.cpp [ 62%] Linking CXX static library libcmaple_model.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/model && /usr/bin/cmake -P CMakeFiles/cmaple_model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_model.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-15" qc libcmaple_model.a CMakeFiles/cmaple_model.dir/model.cpp.o CMakeFiles/cmaple_model.dir/modelbase.cpp.o CMakeFiles/cmaple_model.dir/model_dna.cpp.o CMakeFiles/cmaple_model.dir/model_aa.cpp.o CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o "/usr/bin/gcc-ranlib-15" libcmaple_model.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 62%] Built target cmaple_model [ 62%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelfactory.cpp [ 63%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 63%] Built target pda make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/tree/CMakeFiles/cmaple_tree.dir/DependInfo.cmake "--color=" cmaple_tree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/tree && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o -MF CMakeFiles/cmaple_tree.dir/tree.cpp.o.d -o CMakeFiles/cmaple_tree.dir/tree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/tree.cpp [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/tree && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/tree.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:34: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:319:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 319 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 65%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelprotein.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelset.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h: In function ‘cmaple::initLhVecMerge<(unsigned short)20>(unsigned short, double, cmaple::ModelBase const*, bool, std::unique_ptr, std::default_delete > > const&)std::array’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1617 | output_lh_vec[i] = equal_prob; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop 1616 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ [ 65%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/tree && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -MF CMakeFiles/cmaple_tree.dir/phylonode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h: In function ‘cmaple::do_merge_ORACGT_ORACGT<(unsigned short)20>(cmaple::SeqRegion const&, cmaple::SeqRegion const&, double, double, double, int, cmaple::Alignment const*, cmaple::ModelBase const*, double, std::unique_ptr >&, bool, double&)bool’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1872:35: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1872 | seq1_lh_vec[i] *= model->root_freqs[i]; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1870:35: note: within this loop 1870 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1940 | total_prob += merged_lh_vec[i]; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop 1939 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 65%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelsubst.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/partitionmodel.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/partitionmodelplen.cpp [ 66%] Linking CXX static library libcmaple_tree.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/tree && /usr/bin/cmake -P CMakeFiles/cmaple_tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_tree.dir/link.txt --verbose=1 "/usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 66%] Built target cmaple_tree make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/maple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/maple/CMakeFiles/maple.dir/DependInfo.cmake "--color=" maple make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 66%] Building CXX object cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/maple && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o -MF CMakeFiles/maple.dir/cmaple.cpp.o.d -o CMakeFiles/maple.dir/cmaple.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rategamma.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 67%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rategammainvar.cpp [ 68%] Linking CXX static library libmaple.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/maple && /usr/bin/cmake -P CMakeFiles/maple.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/maple && /usr/bin/cmake -E cmake_link_script CMakeFiles/maple.dir/link.txt --verbose=1 "/usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 68%] Built target maple [ 68%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgamma.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratecontinuousgamma.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratecontinuousgammainvar.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rateheterogeneity.cpp make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple/CMakeFiles/cmaple.dir/DependInfo.cmake "--color=" cmaple make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 70%] Building CXX object cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o -MF CMakeFiles/cmaple.dir/main/main.cpp.o.d -o CMakeFiles/cmaple.dir/main/main.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/main.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rateinvar.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratemeyerdiscrete.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/main.cpp:32: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 71%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratemeyerhaeseler.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratekategory.cpp [ 71%] Linking CXX executable cmaple cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple.dir/link.txt --verbose=1 [ 71%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratefree.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratefreeinvar.cpp tree/./cmaple/tree/../alignment/../model/../utils/matrix.h: In function ‘mul4’: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:132:22: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1793:38, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2137:51: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1783:8, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2137:51: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1160:54, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1425:35: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1125:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1425:35: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_RACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1230:51, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1305:34, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1431:39: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1262:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1431:39: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ [ 72%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rateheterotachy.cpp tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: tree/./cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] tree/./cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘initLhVecMerge’ at tree/./cmaple/tree/../alignment/seqregions.h:1589:46: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: tree/./cmaple/tree/../alignment/seqregions.h:535:1: note: destination object ‘output_lh_vec’ of size 32 [ 72%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rateheterotachyinvar.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelcodon.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelmorphology.cpp In function ‘do_merge_ORACGT_ORACGT’, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] tree/./cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1931:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:36: note: destination object ‘seq2_lh_vec’ of size 32 [ 73%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelmixture.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelunrest.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelliemarkov.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelpomo.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelpomomixture.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--dependency-file=CMakeFiles/cmaple.dir/link.d CMakeFiles/cmaple.dir/main/main.cpp.o -o cmaple -L/build/reproducible-path/iqtree3-3.1.1+dfsg/lib -L/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/libraries/static/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+dfsg/lib:/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/libraries/static/lib maple/libmaple.a tree/libcmaple_tree.a model/libcmaple_model.a ../ncl/libncl.a ../nclextra/libnclextra.a alignment/libcmaple_alignment.a utils/libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 74%] Built target cmaple [ 75%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelfactorymixlen.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelhmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmm.cpp.o -MF CMakeFiles/model.dir/modelhmm.cpp.o.d -o CMakeFiles/model.dir/modelhmm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelhmm.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelhmmgm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmgm.cpp.o -MF CMakeFiles/model.dir/modelhmmgm.cpp.o.d -o CMakeFiles/model.dir/modelhmmgm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelhmmgm.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelhmmtm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmtm.cpp.o -MF CMakeFiles/model.dir/modelhmmtm.cpp.o.d -o CMakeFiles/model.dir/modelhmmtm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelhmmtm.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelcodonmixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodonmixture.cpp.o -MF CMakeFiles/model.dir/modelcodonmixture.cpp.o.d -o CMakeFiles/model.dir/modelcodonmixture.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelcodonmixture.cpp [ 76%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modeldnaerror.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o CMakeFiles/model.dir/modelhmm.cpp.o CMakeFiles/model.dir/modelhmmgm.cpp.o CMakeFiles/model.dir/modelhmmtm.cpp.o CMakeFiles/model.dir/modelcodonmixture.cpp.o /usr/bin/ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 76%] Built target model make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/simulator /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/simulator/CMakeFiles/simulator.dir/DependInfo.cmake "--color=" simulator make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator/alisimulatorheterogeneityinvar.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/simulator && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator/alisimulatorheterogeneity.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/simulator && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator/alisimulatorinvar.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/simulator && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o -MF CMakeFiles/simulator.dir/alisimulator.cpp.o.d -o CMakeFiles/simulator.dir/alisimulator.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator/alisimulator.cpp [ 78%] Linking CXX static library libsimulator.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/simulator && /usr/bin/cmake -P CMakeFiles/simulator.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/simulator && /usr/bin/cmake -E cmake_link_script CMakeFiles/simulator.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 78%] Built target simulator make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" alignment make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/substitution.cpp.o [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/substitution.cpp.o -MF CMakeFiles/alignment.dir/substitution.cpp.o.d -o CMakeFiles/alignment.dir/substitution.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/substitution.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/pattern.cpp [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o -MF CMakeFiles/alignment.dir/alignmentsummary.cpp.o.d -o CMakeFiles/alignment.dir/alignmentsummary.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/alignmentsummary.cpp [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/alignmentpairwise.cpp [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/maalignment.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/alignment.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/superalignment.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/superalignmentpairwise.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/superalignmentpairwiseplen.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/superalignmentunlinked.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequence.cpp.o -MF CMakeFiles/alignment.dir/sequence.cpp.o.d -o CMakeFiles/alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/sequence.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -MF CMakeFiles/alignment.dir/sequencechunkstr.cpp.o.d -o CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/sequencechunkstr.cpp [ 83%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 83%] Built target alignment make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color=" tree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/constrainttree.cpp [ 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/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/candidateset.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/iqtree.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemix.cpp.o -MF CMakeFiles/tree.dir/iqtreemix.cpp.o.d -o CMakeFiles/tree.dir/iqtreemix.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/iqtreemix.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -MF CMakeFiles/tree.dir/iqtreemixhmm.cpp.o.d -o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/iqtreemixhmm.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/matree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/memslot.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/mexttree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/mtree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/mtreeset.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/ncbitree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/node.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/genomenode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genomenode.cpp.o -MF CMakeFiles/tree.dir/genomenode.cpp.o.d -o CMakeFiles/tree.dir/genomenode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/genomenode.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/genometree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genometree.cpp.o -MF CMakeFiles/tree.dir/genometree.cpp.o.d -o CMakeFiles/tree.dir/genometree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/genometree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylonode.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylonodemixlen.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosuperhmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosuperhmm.cpp.o -MF CMakeFiles/tree.dir/phylosuperhmm.cpp.o.d -o CMakeFiles/tree.dir/phylosuperhmm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosuperhmm.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosupertree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosupertreeplen.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosupertreeunlinked.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylotree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylotreemixlen.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylotreepars.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylotreesse.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/quartet.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/supernode.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/tinatree.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/parstree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylohmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/discordance.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylohmm.cpp.o -MF CMakeFiles/tree.dir/phylohmm.cpp.o.d -o CMakeFiles/tree.dir/phylohmm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylohmm.cpp [ 93%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/iqtreemix.cpp.o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/genomenode.cpp.o CMakeFiles/tree.dir/genometree.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosuperhmm.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o CMakeFiles/tree.dir/discordance.cpp.o CMakeFiles/tree.dir/phylohmm.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 93%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terrace /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color=" terrace make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terracetphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terracetphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terracetphast/CMakeFiles/terracetphast.dir/DependInfo.cmake "--color=" terracetphast make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 93%] Building CXX object terrace/CMakeFiles/terrace.dir/terracetree.cpp.o [ 94%] Building CXX object terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o [ 94%] Building CXX object terrace/CMakeFiles/terrace.dir/terracenode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracetree.cpp.o -MF CMakeFiles/terrace.dir/terracetree.cpp.o.d -o CMakeFiles/terrace.dir/terracetree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace/terracetree.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -MF CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o.d -o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace/presenceabsencematrix.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracenode.cpp.o -MF CMakeFiles/terrace.dir/terracenode.cpp.o.d -o CMakeFiles/terrace.dir/terracenode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace/terracenode.cpp [ 94%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace/terrace.cpp [ 95%] Building CXX object terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o -MF CMakeFiles/terracetphast.dir/terracetphast.cpp.o.d -o CMakeFiles/terracetphast.dir/terracetphast.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terracetphast/terracetphast.cpp [ 95%] Linking CXX static library libterracetphast.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terracetphast && /usr/bin/cmake -P CMakeFiles/terracetphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terracetphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terracetphast.dir/link.txt --verbose=1 /usr/bin/ar qc libterracetphast.a CMakeFiles/terracetphast.dir/terracetphast.cpp.o /usr/bin/ranlib libterracetphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 95%] Built target terracetphast [ 95%] Linking CXX static library libterrace.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 95%] Built target terrace make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/main /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/main /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" main make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [ 95%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o [ 95%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o [ 96%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/main.cpp [ 96%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o [ 96%] Building CXX object main/CMakeFiles/main.dir/alisim.cpp.o [ 97%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/timetree.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/treetesting.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/alisim.cpp.o -MF CMakeFiles/main.dir/alisim.cpp.o.d -o CMakeFiles/main.dir/alisim.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/alisim.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/main/main.cpp:132:25: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 132 | out << " built " << __DATE__; | ^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp:1451:53: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 1451 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/main.cpp:52: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/alisim.h:15, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/alisim.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp: In function ‘char* initFreqSet(PML::SeqType)’: /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6288:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6288 | case SEQ_CODON: return ",F1X4,F3X4"; | ^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6289:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6289 | case SEQ_MORPH: return "FQ"; | ^~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6290:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6290 | case SEQ_PROTEIN: return ",FO"; | ^~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6291:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6291 | default: return "FO"; | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 98%] Building CXX object main/CMakeFiles/main.dir/terraceanalysis.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/terraceanalysis.cpp.o -MF CMakeFiles/main.dir/terraceanalysis.cpp.o.d -o CMakeFiles/main.dir/terraceanalysis.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/terraceanalysis.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp:32: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 98%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.omp' [ 98%] Built target main make -f CMakeFiles/iqtree3.dir/build.make CMakeFiles/iqtree3.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/CMakeFiles/iqtree3.dir/DependInfo.cmake "--color=" iqtree3 make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' make -f CMakeFiles/iqtree3.dir/build.make CMakeFiles/iqtree3.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [100%] Building CXX object CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree3 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree3.dir/link.txt --verbose=1 cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h: In function ‘mul4’: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:132:22: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘initLhVecMerge’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1589:46: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:535:1: note: destination object ‘output_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1793:38, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2137:51: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1783:8, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2137:51: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1160:54, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1425:35: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1125:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1425:35: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_RACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1230:51, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1305:34, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1431:39: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1262:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1431:39: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘do_merge_ORACGT_ORACGT’, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1931:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:36: note: destination object ‘seq2_lh_vec’ of size 32 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/iqtree3.dir/link.d CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o -o iqtree3 -L/build/reproducible-path/iqtree3-3.1.1+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+dfsg/lib: booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a simulator/libsimulator.a terrace/libterrace.a -lyaml-cpp phylo-yaml/libphyloYAML.a main/libmain.a cmaple/maple/libmaple.a -lm terracetphast/libterracetphast.a lsd2/liblsd2.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a -lyaml-cpp booster/libbooster.a pda/libpda.a whtest/libwhtest.a vectorclass/libvectorclass.a terrace/libterrace.a cmaple/tree/libcmaple_tree.a cmaple/model/libcmaple_model.a nclextra/libnclextra.a cmaple/alignment/libcmaple_alignment.a cmaple/utils/libcmaple_utils.a tree/libtree.a pll/libpll.a alignment/libalignment.a simulator/libsimulator.a alignment/libalignment.a simulator/libsimulator.a ncl/libncl.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a /usr/lib/x86_64-linux-gnu/libz.so gsl/libgsl.a terraphast/libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' [100%] Built target iqtree3 make[3]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree3 ] ; then mv build.omp/iqtree3 build.omp/iqtree3-omp ; fi dh_auto_build -Bbuild.serial cd build.serial && make -j6 INSTALL="install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' /usr/bin/cmake -S/build/reproducible-path/iqtree3-3.1.1+dfsg -B/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/CMakeFiles /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/depend make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" kernelsse make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" kernelavx make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" kernelfma make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/booster /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" booster make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2 /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lsd2 /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lsd2/CMakeFiles/lsd2.dir/DependInfo.cmake "--color=" lsd2 make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" pll make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 0%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylotreeavx.cpp make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/build /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylokernelsse.cpp make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 1%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/bitset_index.c [ 2%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/alignment.c [ 3%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -MF CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o.d -o CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/confidence_interval.cpp [ 3%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylokernelfma.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 3%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/hashmap.c [ 3%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c [ 4%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/io.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c:43: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c:326:3: note: in expansion of macro ‘rax_posix_memalign’ 326 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 4%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/sort.c [ 4%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/tree.c [ 4%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluateGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluateGenericSpecial.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 5%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/booster.c [ 5%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/hashtables_bfields.c [ 6%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:1173:3: note: in expansion of macro ‘rax_posix_memalign’ 1173 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:1015:3: note: in expansion of macro ‘rax_posix_memalign’ 1015 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:1324:3: note: in expansion of macro ‘rax_posix_memalign’ 1324 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:934:3: note: in expansion of macro ‘rax_posix_memalign’ 934 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 6%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/prng.c [ 7%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/stats.c [ 7%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:115: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:1701:7: note: in expansion of macro ‘rax_posix_memalign’ 1701 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:1777:3: note: in expansion of macro ‘rax_posix_memalign’ 1777 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/tree_utils.c [ 7%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 7%] Built target booster [ 7%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/hardware.c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/hardware.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 8%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/hash.c [ 8%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/ncl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" ncl cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/lexer.c make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 9%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsassumptionsblock.cpp [ 9%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:41: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:2686:3: note: in expansion of macro ‘rax_posix_memalign’ 2686 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:3061:3: note: in expansion of macro ‘rax_posix_memalign’ 3061 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/models.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/models.c:47: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsblock.cpp [ 10%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newick.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxscharactersblock.cpp [ 10%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c [ 10%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o -MF CMakeFiles/lsd2.dir/src/dating.cpp.o.d -o CMakeFiles/lsd2.dir/src/dating.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/dating.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:46: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:2766:13: note: in expansion of macro ‘rax_posix_memalign’ 2766 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:2795:17: note: in expansion of macro ‘rax_posix_memalign’ 2795 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:3733:11: note: in expansion of macro ‘rax_posix_memalign’ 3733 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:3803:3: note: in expansion of macro ‘rax_posix_memalign’ 3803 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -MF CMakeFiles/lsd2.dir/src/estimate_root.cpp.o.d -o CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/estimate_root.cpp [ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsdatablock.cpp [ 12%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/genericParallelization.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 12%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/optimizeModel.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/optimizeModel.c:44: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsdiscretedatum.cpp [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsdiscretematrix.cpp [ 13%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o -MF CMakeFiles/lsd2.dir/src/lsd.cpp.o.d -o CMakeFiles/lsd2.dir/src/lsd.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/lsd.cpp [ 13%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/parsePartition.c [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsdistancedatum.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 15%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/queue.c [ 15%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/randomTree.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 15%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/recom.c:41: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/restartHashTable.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/restartHashTable.c:41: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o [ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsdistancesblock.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/searchAlgo.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/searchAlgo.c:45: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 16%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o -MF CMakeFiles/lsd2.dir/src/options.cpp.o.d -o CMakeFiles/lsd2.dir/src/options.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp [ 16%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/ssort.c [ 17%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/stack.c [ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o [ 17%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsemptyblock.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/topologies.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/topologies.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/trash.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp: In function ‘Pr* getInterface()’: /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:306:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 306 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:311:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 311 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:338:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 338 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:342:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp: In function ‘void setOptionsWithLetter(Pr*, char)’: /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:872:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 872 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:877:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:923:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 923 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/treeIO.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/treeIO.c:41: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:67: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:44: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:596:7: note: in expansion of macro ‘rax_posix_memalign’ 596 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:597:7: note: in expansion of macro ‘rax_posix_memalign’ 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:599:7: note: in expansion of macro ‘rax_posix_memalign’ 599 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:605:7: note: in expansion of macro ‘rax_posix_memalign’ 605 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:617:15: note: in expansion of macro ‘rax_posix_memalign’ 617 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:621:15: note: in expansion of macro ‘rax_posix_memalign’ 621 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:687:7: note: in expansion of macro ‘rax_posix_memalign’ 687 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:694:7: note: in expansion of macro ‘rax_posix_memalign’ 694 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:724:7: note: in expansion of macro ‘rax_posix_memalign’ 724 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:744:7: note: in expansion of macro ‘rax_posix_memalign’ 744 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:756:11: note: in expansion of macro ‘rax_posix_memalign’ 756 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsexception.cpp [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsreader.cpp [ 20%] Linking C static library libpll.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 20%] Built target pll [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxssetreader.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsstring.cpp [ 21%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o -MF CMakeFiles/lsd2.dir/src/outliers.cpp.o.d -o CMakeFiles/lsd2.dir/src/outliers.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/outliers.cpp [ 22%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o -MF CMakeFiles/lsd2.dir/src/readData.cpp.o.d -o CMakeFiles/lsd2.dir/src/readData.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/readData.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxstaxablock.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxstoken.cpp [ 22%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o -MF CMakeFiles/lsd2.dir/src/utils.cpp.o.d -o CMakeFiles/lsd2.dir/src/utils.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/utils.cpp [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxstreesblock.cpp make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/nclextra /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" nclextra make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra/mpdablock.cpp [ 23%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 23%] Built target ncl [ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra/msetsblock.cpp [ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra/msplitsblock.cpp [ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra/modelsblock.cpp make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/sprng /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" sprng make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 24%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/lcg64.c [ 24%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/makeseed.c [ 24%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/memory.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/store.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/primes-lcg64.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/checkid.c [ 26%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 26%] Built target sprng make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/lbfgsb /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lbfgsb /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" lbfgsb make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 26%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lbfgsb/lbfgsb_new.cpp [ 27%] Linking CXX static library libnclextra.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 27%] Built target nclextra make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/whtest /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" whtest make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 27%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/eigen.c [ 27%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/eigen_sym.c [ 27%] Linking CXX static library liblsd2.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lsd2 && /usr/bin/cmake -P CMakeFiles/lsd2.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lsd2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/lsd2.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 27%] Built target lsd2 make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/vectorclass /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/vectorclass /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" vectorclass [ 28%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/random.c make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 28%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/vectorclass/instrset_detect.cpp [ 29%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 29%] Built target vectorclass [ 29%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/weisslambda.c [ 29%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/weisslambda_sub.c [ 30%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest.c [ 30%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 30%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_wrapper.cpp make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/gsl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" gsl make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 30%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/binomial_tpe.cpp [ 30%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/multinomial.cpp [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/pow_int.cpp [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/gauss.cpp [ 31%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 31%] Built target lbfgsb make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/utils/CMakeFiles/cmaple_utils.dir/DependInfo.cmake "--color=" cmaple_utils make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 32%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/utils && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o -MF CMakeFiles/cmaple_utils.dir/tools.cpp.o.d -o CMakeFiles/cmaple_utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/tools.cpp [ 32%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/gaussinv.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/tools.cpp:44:23: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 44 | out << " built " << __DATE__ << std::endl; | ^~~~~~~~ [ 33%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 33%] Built target whtest [ 34%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" pllavx cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/gausspdf.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 35%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/avxLikelihood.c [ 35%] Linking CXX static library libgsl.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 35%] Built target gsl make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/phylo-yaml /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/phylo-yaml /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" phyloYAML make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 35%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/phylo-yaml/statespace.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/avxLikelihood.c:60: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 35%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/utils && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -MF CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/operatingsystem.cpp [ 35%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/utils && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/gzstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/gzstream.cpp [ 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 [ 35%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 35%] Built target pllavx make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" terraphast /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/iqtree3-3.1.1+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 35%] Built target kernelsse [ 35%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/advanced.cpp [ 36%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/utils && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/logstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/logstream.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/logstream.cpp make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/utils/CMakeFiles/decentTree.dir/DependInfo.cmake "--color=" decentTree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 36%] Building CXX object utils/CMakeFiles/decentTree.dir/decenttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/decenttree.cpp.o -MF CMakeFiles/decentTree.dir/decenttree.cpp.o.d -o CMakeFiles/decentTree.dir/decenttree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/decenttree.cpp [ 37%] Building CXX object utils/CMakeFiles/decentTree.dir/starttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/starttree.cpp.o -MF CMakeFiles/decentTree.dir/starttree.cpp.o.d -o CMakeFiles/decentTree.dir/starttree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/starttree.cpp [ 37%] Linking CXX static library libcmaple_utils.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/utils && /usr/bin/cmake -P CMakeFiles/cmaple_utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_utils.dir/link.txt --verbose=1 "/usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 37%] Built target cmaple_utils [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/bigint.cpp [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/bipartitions.cpp [ 38%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj.cpp.o -MF CMakeFiles/decentTree.dir/bionj.cpp.o.d -o CMakeFiles/decentTree.dir/bionj.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/bionj.cpp [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/bitmatrix.cpp [ 38%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj2.cpp.o -MF CMakeFiles/decentTree.dir/bionj2.cpp.o.d -o CMakeFiles/decentTree.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/bionj2.cpp [ 40%] Building CXX object utils/CMakeFiles/decentTree.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/gzstream.cpp.o -MF CMakeFiles/decentTree.dir/gzstream.cpp.o.d -o CMakeFiles/decentTree.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/gzstream.cpp [ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/clamped_uint.cpp [ 41%] Building CXX object utils/CMakeFiles/decentTree.dir/progress.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/progress.cpp.o -MF CMakeFiles/decentTree.dir/progress.cpp.o.d -o CMakeFiles/decentTree.dir/progress.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/progress.cpp [ 41%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 41%] Built target phyloYAML [ 41%] Building CXX object utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o [ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o -MF CMakeFiles/decentTree.dir/operatingsystem.cpp.o.d -o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/operatingsystem.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/constraints.cpp make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" utils make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 42%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/eigendecomposition.cpp [ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/errors.cpp [ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/multitree.cpp make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pda /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pda /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" pda make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 43%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/circularnetwork.cpp [ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/multitree_iterator.cpp [ 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 [ 43%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/nodes.cpp /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/iqtree3-3.1.1+dfsg/build.serial' [ 43%] Built target kernelfma make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/alignment/CMakeFiles/cmaple_alignment.dir/DependInfo.cmake "--color=" cmaple_alignment make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 43%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/alignment && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -MF CMakeFiles/cmaple_alignment.dir/mutation.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/mutation.cpp [ 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/iqtree3-3.1.1+dfsg/build.serial' [ 44%] Built target kernelavx [ 44%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/gzstream.cpp [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/parser.cpp [ 45%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/optimization.cpp [ 45%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/greedy.cpp [ 46%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/alignment && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregion.cpp [ 47%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/gurobiwrapper.cpp [ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/rooting.cpp [ 48%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/stoprule.cpp [ 48%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/hashsplitset.cpp [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/simple.cpp [ 49%] Linking CXX executable decentTree cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/decentTree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/decentTree.dir/link.d CMakeFiles/decentTree.dir/decenttree.cpp.o CMakeFiles/decentTree.dir/starttree.cpp.o CMakeFiles/decentTree.dir/bionj.cpp.o CMakeFiles/decentTree.dir/bionj2.cpp.o CMakeFiles/decentTree.dir/gzstream.cpp.o CMakeFiles/decentTree.dir/progress.cpp.o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -o decentTree -L/build/reproducible-path/iqtree3-3.1.1+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+dfsg/lib /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 49%] Built target decentTree [ 49%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/alignment && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.cpp [ 49%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/alignment && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.cpp [ 49%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/pdnetwork.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/subtree_extraction.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/supertree_helpers.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 50%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/tools.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/trees.cpp [ 51%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/alignment && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -MF CMakeFiles/cmaple_alignment.dir/sequence.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.cpp [ 51%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/pllnni.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.h:3, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 52%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/checkpoint.cpp [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/union_find.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 53%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/alignment && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -MF CMakeFiles/cmaple_alignment.dir/alignment.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.cpp [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/validation.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 53%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/MPIHelper.cpp [ 53%] Building CXX object utils/CMakeFiles/utils.dir/starttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/starttree.cpp.o -MF CMakeFiles/utils.dir/starttree.cpp.o.d -o CMakeFiles/utils.dir/starttree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/starttree.cpp [ 53%] Linking CXX static library libterraphast.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 53%] Built target terraphast [ 54%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/pruning.cpp [ 54%] Linking CXX static library libcmaple_alignment.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/alignment && /usr/bin/cmake -P CMakeFiles/cmaple_alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_alignment.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-15" qc libcmaple_alignment.a CMakeFiles/cmaple_alignment.dir/mutation.cpp.o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o "/usr/bin/gcc-ranlib-15" libcmaple_alignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 54%] Built target cmaple_alignment [ 54%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/split.cpp [ 55%] Building CXX object utils/CMakeFiles/utils.dir/bionj.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj.cpp.o -MF CMakeFiles/utils.dir/bionj.cpp.o.d -o CMakeFiles/utils.dir/bionj.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/bionj.cpp make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/model/CMakeFiles/cmaple_model.dir/DependInfo.cmake "--color=" cmaple_model make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 55%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/model && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o -MF CMakeFiles/cmaple_model.dir/model.cpp.o.d -o CMakeFiles/cmaple_model.dir/model.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.cpp [ 55%] Building CXX object utils/CMakeFiles/utils.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj2.cpp.o -MF CMakeFiles/utils.dir/bionj2.cpp.o.d -o CMakeFiles/utils.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/bionj2.cpp [ 55%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/splitgraph.cpp [ 55%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/model && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o -MF CMakeFiles/cmaple_model.dir/modelbase.cpp.o.d -o CMakeFiles/cmaple_model.dir/modelbase.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/modelbase.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/splitset.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 56%] Building CXX object utils/CMakeFiles/utils.dir/progress.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/progress.cpp.o -MF CMakeFiles/utils.dir/progress.cpp.o.d -o CMakeFiles/utils.dir/progress.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/progress.cpp [ 56%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/lpwrapper.c [ 57%] Building CXX object utils/CMakeFiles/utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/operatingsystem.cpp.o -MF CMakeFiles/utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/operatingsystem.cpp [ 58%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/model && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o -MF CMakeFiles/cmaple_model.dir/model_dna.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_dna.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/ecopd.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/modelbase.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 58%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/model && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o -MF CMakeFiles/cmaple_model.dir/model_aa.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_aa.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 58%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/graph.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/pdtree.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/pdtreeset.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:34: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:319:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 319 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ [ 60%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/model && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o -MF CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/ecopdmtreeset.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.h:3, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 61%] Linking CXX static library libcmaple_model.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/model && /usr/bin/cmake -P CMakeFiles/cmaple_model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_model.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-15" qc libcmaple_model.a CMakeFiles/cmaple_model.dir/model.cpp.o CMakeFiles/cmaple_model.dir/modelbase.cpp.o CMakeFiles/cmaple_model.dir/model_dna.cpp.o CMakeFiles/cmaple_model.dir/model_aa.cpp.o CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o "/usr/bin/gcc-ranlib-15" libcmaple_model.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 61%] Built target cmaple_model make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/tree/CMakeFiles/cmaple_tree.dir/DependInfo.cmake "--color=" cmaple_tree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 61%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o [ 61%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/tree && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/tree && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o -MF CMakeFiles/cmaple_tree.dir/tree.cpp.o.d -o CMakeFiles/cmaple_tree.dir/tree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/tree.cpp [ 62%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/tree && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.cpp [ 62%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 62%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" model make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 62%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelmarkov.cpp [ 62%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelbin.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 63%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 [ 63%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/tree && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -MF CMakeFiles/cmaple_tree.dir/phylonode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.cpp [ 64%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modeldna.cpp /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/iqtree3-3.1.1+dfsg/build.serial' [ 64%] Built target pda [ 64%] Building CXX object model/CMakeFiles/model.dir/modeldnaerror.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldnaerror.cpp.o -MF CMakeFiles/model.dir/modeldnaerror.cpp.o.d -o CMakeFiles/model.dir/modeldnaerror.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modeldnaerror.cpp [ 64%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelfactory.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/tree.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 65%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelprotein.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:34: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:319:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 319 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ [ 65%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelset.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h: In function ‘cmaple::initLhVecMerge<(unsigned short)20>(unsigned short, double, cmaple::ModelBase const*, bool, std::unique_ptr, std::default_delete > > const&)std::array’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1617 | output_lh_vec[i] = equal_prob; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop 1616 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ [ 65%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelsubst.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h: In function ‘cmaple::do_merge_ORACGT_ORACGT<(unsigned short)20>(cmaple::SeqRegion const&, cmaple::SeqRegion const&, double, double, double, int, cmaple::Alignment const*, cmaple::ModelBase const*, double, std::unique_ptr >&, bool, double&)bool’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1872:35: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1872 | seq1_lh_vec[i] *= model->root_freqs[i]; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1870:35: note: within this loop 1870 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1940 | total_prob += merged_lh_vec[i]; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop 1939 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ [ 66%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/partitionmodel.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/partitionmodelplen.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rategamma.cpp [ 66%] Linking CXX static library libcmaple_tree.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/tree && /usr/bin/cmake -P CMakeFiles/cmaple_tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_tree.dir/link.txt --verbose=1 "/usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 66%] Built target cmaple_tree make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/maple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/maple/CMakeFiles/maple.dir/DependInfo.cmake "--color=" maple make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 66%] Building CXX object cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/maple && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o -MF CMakeFiles/maple.dir/cmaple.cpp.o.d -o CMakeFiles/maple.dir/cmaple.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rategammainvar.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 68%] Linking CXX static library libmaple.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/maple && /usr/bin/cmake -P CMakeFiles/maple.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/maple && /usr/bin/cmake -E cmake_link_script CMakeFiles/maple.dir/link.txt --verbose=1 "/usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 68%] Built target maple make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple/CMakeFiles/cmaple.dir/DependInfo.cmake "--color=" cmaple make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 69%] Building CXX object cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o -MF CMakeFiles/cmaple.dir/main/main.cpp.o.d -o CMakeFiles/cmaple.dir/main/main.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/main.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgamma.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratecontinuousgamma.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratecontinuousgammainvar.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rateheterogeneity.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/main.cpp:32: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 70%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rateinvar.cpp [ 70%] Linking CXX executable cmaple cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple.dir/link.txt --verbose=1 [ 70%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratemeyerdiscrete.cpp tree/./cmaple/tree/../alignment/../model/../utils/matrix.h: In function ‘mul4’: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:132:22: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1793:38, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2137:51: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1783:8, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2137:51: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1160:54, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1425:35: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1125:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1425:35: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_RACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1230:51, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1305:34, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1431:39: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1262:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1431:39: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ [ 71%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratemeyerhaeseler.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratekategory.cpp tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: tree/./cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] tree/./cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘initLhVecMerge’ at tree/./cmaple/tree/../alignment/seqregions.h:1589:46: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: tree/./cmaple/tree/../alignment/seqregions.h:535:1: note: destination object ‘output_lh_vec’ of size 32 [ 71%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratefree.cpp In function ‘do_merge_ORACGT_ORACGT’, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] tree/./cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1931:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:36: note: destination object ‘seq2_lh_vec’ of size 32 [ 72%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratefreeinvar.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rateheterotachy.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rateheterotachyinvar.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelcodon.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelmorphology.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelmixture.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelunrest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--dependency-file=CMakeFiles/cmaple.dir/link.d CMakeFiles/cmaple.dir/main/main.cpp.o -o cmaple -L/build/reproducible-path/iqtree3-3.1.1+dfsg/lib -L/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/libraries/static/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+dfsg/lib:/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/libraries/static/lib maple/libmaple.a tree/libcmaple_tree.a model/libcmaple_model.a ../ncl/libncl.a ../nclextra/libnclextra.a alignment/libcmaple_alignment.a utils/libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 73%] Built target cmaple [ 74%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelliemarkov.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelpomo.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelpomomixture.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelfactorymixlen.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelhmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmm.cpp.o -MF CMakeFiles/model.dir/modelhmm.cpp.o.d -o CMakeFiles/model.dir/modelhmm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelhmm.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelhmmgm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmgm.cpp.o -MF CMakeFiles/model.dir/modelhmmgm.cpp.o.d -o CMakeFiles/model.dir/modelhmmgm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelhmmgm.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelhmmtm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmtm.cpp.o -MF CMakeFiles/model.dir/modelhmmtm.cpp.o.d -o CMakeFiles/model.dir/modelhmmtm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelhmmtm.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelcodonmixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodonmixture.cpp.o -MF CMakeFiles/model.dir/modelcodonmixture.cpp.o.d -o CMakeFiles/model.dir/modelcodonmixture.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelcodonmixture.cpp [ 76%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modeldnaerror.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o CMakeFiles/model.dir/modelhmm.cpp.o CMakeFiles/model.dir/modelhmmgm.cpp.o CMakeFiles/model.dir/modelhmmtm.cpp.o CMakeFiles/model.dir/modelcodonmixture.cpp.o /usr/bin/ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 76%] Built target model make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/simulator /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/simulator/CMakeFiles/simulator.dir/DependInfo.cmake "--color=" simulator make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o -MF CMakeFiles/simulator.dir/alisimulator.cpp.o.d -o CMakeFiles/simulator.dir/alisimulator.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator/alisimulator.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/simulator && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator/alisimulatorinvar.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/simulator && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator/alisimulatorheterogeneity.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/simulator && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator/alisimulatorheterogeneityinvar.cpp [ 78%] Linking CXX static library libsimulator.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/simulator && /usr/bin/cmake -P CMakeFiles/simulator.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/simulator && /usr/bin/cmake -E cmake_link_script CMakeFiles/simulator.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 78%] Built target simulator make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" alignment make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/substitution.cpp.o [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/substitution.cpp.o -MF CMakeFiles/alignment.dir/substitution.cpp.o.d -o CMakeFiles/alignment.dir/substitution.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/substitution.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/pattern.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/alignment.cpp [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o -MF CMakeFiles/alignment.dir/alignmentsummary.cpp.o.d -o CMakeFiles/alignment.dir/alignmentsummary.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/alignmentsummary.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/maalignment.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/alignmentpairwise.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/superalignment.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/superalignmentpairwise.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/superalignmentpairwiseplen.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/superalignmentunlinked.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequence.cpp.o -MF CMakeFiles/alignment.dir/sequence.cpp.o.d -o CMakeFiles/alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/sequence.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -MF CMakeFiles/alignment.dir/sequencechunkstr.cpp.o.d -o CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/sequencechunkstr.cpp [ 83%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 83%] Built target alignment make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color=" tree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 84%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/constrainttree.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/candidateset.cpp [ 84%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/iqtree.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemix.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemix.cpp.o -MF CMakeFiles/tree.dir/iqtreemix.cpp.o.d -o CMakeFiles/tree.dir/iqtreemix.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/iqtreemix.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -MF CMakeFiles/tree.dir/iqtreemixhmm.cpp.o.d -o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/iqtreemixhmm.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/matree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/memslot.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/mexttree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/mtree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/mtreeset.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/ncbitree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/node.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/genomenode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genomenode.cpp.o -MF CMakeFiles/tree.dir/genomenode.cpp.o.d -o CMakeFiles/tree.dir/genomenode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/genomenode.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/genometree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genometree.cpp.o -MF CMakeFiles/tree.dir/genometree.cpp.o.d -o CMakeFiles/tree.dir/genometree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/genometree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylonode.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylonodemixlen.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosuperhmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosuperhmm.cpp.o -MF CMakeFiles/tree.dir/phylosuperhmm.cpp.o.d -o CMakeFiles/tree.dir/phylosuperhmm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosuperhmm.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosupertree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosupertreeplen.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosupertreeunlinked.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylotree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylotreemixlen.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylotreepars.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylotreesse.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/quartet.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/supernode.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/tinatree.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/parstree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/discordance.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylohmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylohmm.cpp.o -MF CMakeFiles/tree.dir/phylohmm.cpp.o.d -o CMakeFiles/tree.dir/phylohmm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylohmm.cpp [ 93%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/iqtreemix.cpp.o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/genomenode.cpp.o CMakeFiles/tree.dir/genometree.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosuperhmm.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o CMakeFiles/tree.dir/discordance.cpp.o CMakeFiles/tree.dir/phylohmm.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 93%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terrace /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color=" terrace make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terracetphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terracetphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terracetphast/CMakeFiles/terracetphast.dir/DependInfo.cmake "--color=" terracetphast make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 94%] Building CXX object terrace/CMakeFiles/terrace.dir/terracetree.cpp.o [ 94%] Building CXX object terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracetree.cpp.o -MF CMakeFiles/terrace.dir/terracetree.cpp.o.d -o CMakeFiles/terrace.dir/terracetree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace/terracetree.cpp [ 94%] Building CXX object terrace/CMakeFiles/terrace.dir/terracenode.cpp.o [ 94%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracenode.cpp.o -MF CMakeFiles/terrace.dir/terracenode.cpp.o.d -o CMakeFiles/terrace.dir/terracenode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace/terracenode.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace/terrace.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terracetphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o -MF CMakeFiles/terracetphast.dir/terracetphast.cpp.o.d -o CMakeFiles/terracetphast.dir/terracetphast.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terracetphast/terracetphast.cpp [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -MF CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o.d -o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace/presenceabsencematrix.cpp [ 95%] Linking CXX static library libterracetphast.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terracetphast && /usr/bin/cmake -P CMakeFiles/terracetphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terracetphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terracetphast.dir/link.txt --verbose=1 /usr/bin/ar qc libterracetphast.a CMakeFiles/terracetphast.dir/terracetphast.cpp.o /usr/bin/ranlib libterracetphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 95%] Built target terracetphast [ 95%] Linking CXX static library libterrace.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 95%] Built target terrace make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/main /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/main /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" main make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [ 96%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o [ 96%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/main.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp [ 96%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o [ 96%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp [ 97%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/timetree.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/treetesting.cpp [ 97%] Building CXX object main/CMakeFiles/main.dir/alisim.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/alisim.cpp.o -MF CMakeFiles/main.dir/alisim.cpp.o.d -o CMakeFiles/main.dir/alisim.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/alisim.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/main/main.cpp:132:25: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 132 | out << " built " << __DATE__; | ^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp:1451:53: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 1451 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/alisim.h:15, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/alisim.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp: In function ‘char* initFreqSet(PML::SeqType)’: /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6288:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6288 | case SEQ_CODON: return ",F1X4,F3X4"; | ^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6289:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6289 | case SEQ_MORPH: return "FQ"; | ^~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6290:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6290 | case SEQ_PROTEIN: return ",FO"; | ^~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6291:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6291 | default: return "FO"; | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/main.cpp:52: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 98%] Building CXX object main/CMakeFiles/main.dir/terraceanalysis.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/terraceanalysis.cpp.o -MF CMakeFiles/main.dir/terraceanalysis.cpp.o.d -o CMakeFiles/main.dir/terraceanalysis.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/terraceanalysis.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp:32: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 98%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.serial' [ 98%] Built target main make -f CMakeFiles/iqtree3.dir/build.make CMakeFiles/iqtree3.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/CMakeFiles/iqtree3.dir/DependInfo.cmake "--color=" iqtree3 make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make -f CMakeFiles/iqtree3.dir/build.make CMakeFiles/iqtree3.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [100%] Building CXX object CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DNUM_STATES=4 -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree3 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree3.dir/link.txt --verbose=1 cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h: In function ‘mul4’: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:132:22: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘initLhVecMerge’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1589:46: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:535:1: note: destination object ‘output_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1793:38, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2137:51: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1783:8, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2137:51: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1160:54, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1425:35: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1125:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1425:35: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_RACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1230:51, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1305:34, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1431:39: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1262:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1431:39: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘do_merge_ORACGT_ORACGT’, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1931:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:36: note: destination object ‘seq2_lh_vec’ of size 32 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/iqtree3.dir/link.d CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o -o iqtree3 -L/build/reproducible-path/iqtree3-3.1.1+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+dfsg/lib: booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a simulator/libsimulator.a terrace/libterrace.a -lyaml-cpp phylo-yaml/libphyloYAML.a main/libmain.a cmaple/maple/libmaple.a -lm terracetphast/libterracetphast.a lsd2/liblsd2.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a -lyaml-cpp booster/libbooster.a pda/libpda.a whtest/libwhtest.a vectorclass/libvectorclass.a terrace/libterrace.a cmaple/tree/libcmaple_tree.a cmaple/model/libcmaple_model.a nclextra/libnclextra.a cmaple/alignment/libcmaple_alignment.a cmaple/utils/libcmaple_utils.a tree/libtree.a pll/libpll.a alignment/libalignment.a simulator/libsimulator.a alignment/libalignment.a simulator/libsimulator.a ncl/libncl.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a /usr/lib/x86_64-linux-gnu/libz.so gsl/libgsl.a terraphast/libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' [100%] Built target iqtree3 make[3]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree3 ] ; then mv build.omp/iqtree3 build.omp/iqtree3-omp ; fi dh_auto_build -Bbuild.mpi cd build.mpi && make -j6 INSTALL="install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' /usr/bin/cmake -S/build/reproducible-path/iqtree3-3.1.1+dfsg -B/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/CMakeFiles /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/depend make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color=" kernelsse make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake "--color=" kernelavx make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake "--color=" kernelfma make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2 /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lsd2 /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lsd2/CMakeFiles/lsd2.dir/DependInfo.cmake "--color=" lsd2 make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/booster /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/booster /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" booster make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" pll make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f lsd2/CMakeFiles/lsd2.dir/build.make lsd2/CMakeFiles/lsd2.dir/build [ 0%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' /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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylotreeavx.cpp [ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build /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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylokernelfma.cpp make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 1%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o [ 2%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -MF CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o.d -o CMakeFiles/lsd2.dir/src/confidence_interval.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/confidence_interval.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/alignment.c [ 2%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/bitset_index.c [ 3%] 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_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylokernelsse.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/alignment.c:40: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 3%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/hashmap.c [ 3%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c:43: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/bipartitionList.c:326:3: note: in expansion of macro ‘rax_posix_memalign’ 326 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 4%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/io.c [ 4%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/sort.c [ 4%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/tree.c [ 4%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluateGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluateGenericSpecial.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 5%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/booster.c [ 6%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c [ 6%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/hashtables_bfields.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:1173:3: note: in expansion of macro ‘rax_posix_memalign’ 1173 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:1015:3: note: in expansion of macro ‘rax_posix_memalign’ 1015 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:1324:3: note: in expansion of macro ‘rax_posix_memalign’ 1324 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/evaluatePartialGenericSpecial.c:934:3: note: in expansion of macro ‘rax_posix_memalign’ 934 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 6%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/prng.c [ 7%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/stats.c [ 7%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:115: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:1701:7: note: in expansion of macro ‘rax_posix_memalign’ 1701 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/fastDNAparsimony.c:1777:3: note: in expansion of macro ‘rax_posix_memalign’ 1777 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 7%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/booster/tree_utils.c [ 7%] Linking C static library libbooster.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 7%] Built target booster [ 7%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/hardware.c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/hardware.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/ncl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color=" ncl make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 8%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsassumptionsblock.cpp [ 9%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/hash.c [ 9%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/lexer.c [ 9%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:41: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:29: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:2686:3: note: in expansion of macro ‘rax_posix_memalign’ 2686 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/makenewzGenericSpecial.c:3061:3: note: in expansion of macro ‘rax_posix_memalign’ 3061 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/models.c [ 10%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/dating.cpp.o -MF CMakeFiles/lsd2.dir/src/dating.cpp.o.d -o CMakeFiles/lsd2.dir/src/dating.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/dating.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/models.c:47: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsblock.cpp [ 10%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newick.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newick.c:36: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxscharactersblock.cpp [ 10%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:46: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:32: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:2766:13: note: in expansion of macro ‘rax_posix_memalign’ 2766 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:2795:17: note: in expansion of macro ‘rax_posix_memalign’ 2795 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -MF CMakeFiles/lsd2.dir/src/estimate_root.cpp.o.d -o CMakeFiles/lsd2.dir/src/estimate_root.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/estimate_root.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:3733:11: note: in expansion of macro ‘rax_posix_memalign’ 3733 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/newviewGenericSpecial.c:3803:3: note: in expansion of macro ‘rax_posix_memalign’ 3803 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ [ 11%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/genericParallelization.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/genericParallelization.c:43: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 12%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/lsd.cpp.o -MF CMakeFiles/lsd2.dir/src/lsd.cpp.o.d -o CMakeFiles/lsd2.dir/src/lsd.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/lsd.cpp [ 12%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/optimizeModel.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/optimizeModel.c:44: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsdatablock.cpp [ 13%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/parsePartition.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/parsePartition.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 14%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/queue.c [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsdiscretedatum.cpp [ 14%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/randomTree.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/randomTree.c:37: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 14%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/recom.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/recom.c:41: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 15%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/restartHashTable.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/restartHashTable.c:41: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 15%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/searchAlgo.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/searchAlgo.c:45: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsdiscretematrix.cpp [ 15%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/ssort.c [ 15%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/options.cpp.o -MF CMakeFiles/lsd2.dir/src/options.cpp.o.d -o CMakeFiles/lsd2.dir/src/options.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp [ 16%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/stack.c [ 16%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/topologies.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/topologies.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsdistancedatum.cpp [ 17%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/trash.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/trash.c:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/treeIO.c In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/treeIO.c:41: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 18%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp: In function ‘Pr* getInterface()’: /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:306:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 306 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:311:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 311 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:338:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 338 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:342:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp: In function ‘void setOptionsWithLetter(Pr*, char)’: /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:872:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 872 | fgets(letter,3,stdin); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:877:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets( letter1, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/options.cpp:923:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 923 | fgets( letter, 3, stdin ); | ~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:67: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:44: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:596:7: note: in expansion of macro ‘rax_posix_memalign’ 596 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:597:7: note: in expansion of macro ‘rax_posix_memalign’ 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:599:7: note: in expansion of macro ‘rax_posix_memalign’ 599 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:605:7: note: in expansion of macro ‘rax_posix_memalign’ 605 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:617:15: note: in expansion of macro ‘rax_posix_memalign’ 617 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:621:15: note: in expansion of macro ‘rax_posix_memalign’ 621 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:687:7: note: in expansion of macro ‘rax_posix_memalign’ 687 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:694:7: note: in expansion of macro ‘rax_posix_memalign’ 694 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:724:7: note: in expansion of macro ‘rax_posix_memalign’ 724 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:744:7: note: in expansion of macro ‘rax_posix_memalign’ 744 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/mem_alloc.h:37:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | #define rax_posix_memalign posix_memalign /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/utils.c:756:11: note: in expansion of macro ‘rax_posix_memalign’ 756 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsdistancesblock.cpp [ 18%] Linking C static library libpll.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 18%] Built target pll [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsemptyblock.cpp [ 18%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/outliers.cpp.o -MF CMakeFiles/lsd2.dir/src/outliers.cpp.o.d -o CMakeFiles/lsd2.dir/src/outliers.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/outliers.cpp [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsexception.cpp [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsreader.cpp [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxssetreader.cpp make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/nclextra /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" nclextra make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 20%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra/mpdablock.cpp [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxsstring.cpp [ 22%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/readData.cpp.o -MF CMakeFiles/lsd2.dir/src/readData.cpp.o.d -o CMakeFiles/lsd2.dir/src/readData.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/readData.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxstaxablock.cpp [ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra/msetsblock.cpp [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxstoken.cpp [ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra/msplitsblock.cpp [ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/ncl/nxstreesblock.cpp [ 24%] Building CXX object lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lsd2 && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lsd2/CMakeFiles/lsd2.dir/src/utils.cpp.o -MF CMakeFiles/lsd2.dir/src/utils.cpp.o.d -o CMakeFiles/lsd2.dir/src/utils.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lsd2/src/utils.cpp [ 24%] Linking CXX static library libncl.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 24%] Built target ncl make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/sprng /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color=" sprng make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 24%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/lcg64.c [ 24%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/makeseed.c [ 24%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/memory.c [ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/nclextra/modelsblock.cpp [ 25%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/store.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/primes-lcg64.c [ 25%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/sprng/checkid.c [ 26%] Linking C static library libsprng.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 26%] Built target sprng make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/lbfgsb /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lbfgsb /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" lbfgsb make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 26%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/lbfgsb/lbfgsb_new.cpp [ 27%] Linking CXX static library libnclextra.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 27%] Built target nclextra make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/whtest /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color=" whtest make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 27%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/eigen.c [ 27%] Linking CXX static library liblbfgsb.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 27%] Built target lbfgsb make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/vectorclass /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/vectorclass /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" vectorclass make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 27%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/vectorclass/instrset_detect.cpp [ 28%] Linking CXX static library libvectorclass.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 28%] Built target vectorclass [ 28%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/eigen_sym.c [ 29%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/random.c [ 29%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/weisslambda.c [ 29%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/weisslambda_sub.c [ 30%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest.c [ 30%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 30%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/whtest/whtest_wrapper.cpp make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/gsl /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color=" gsl make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 30%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/binomial_tpe.cpp [ 30%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/multinomial.cpp [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/pow_int.cpp [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/gauss.cpp [ 31%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/gaussinv.cpp [ 32%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/gsl/gausspdf.cpp [ 33%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 33%] Built target whtest make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/utils/CMakeFiles/cmaple_utils.dir/DependInfo.cmake "--color=" cmaple_utils make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f cmaple/utils/CMakeFiles/cmaple_utils.dir/build.make cmaple/utils/CMakeFiles/cmaple_utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 34%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/utils && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/tools.cpp.o -MF CMakeFiles/cmaple_utils.dir/tools.cpp.o.d -o CMakeFiles/cmaple_utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/tools.cpp [ 34%] Linking CXX static library libgsl.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 34%] Built target gsl make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" pllavx make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 35%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/avxLikelihood.c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/tools.cpp:44:23: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 44 | out << " built " << __DATE__ << std::endl; | ^~~~~~~~ [ 35%] Linking CXX static library liblsd2.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lsd2 && /usr/bin/cmake -P CMakeFiles/lsd2.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/lsd2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/lsd2.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 35%] Built target lsd2 [ 35%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/utils && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -MF CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/cmaple_utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/operatingsystem.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/avxLikelihood.c:60: /build/reproducible-path/iqtree3-3.1.1+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 35%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/utils && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/gzstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/gzstream.cpp [ 36%] Building CXX object cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/utils && /usr/bin/c++ -DCMAPLE -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/utils/CMakeFiles/cmaple_utils.dir/logstream.cpp.o -MF CMakeFiles/cmaple_utils.dir/logstream.cpp.o.d -o CMakeFiles/cmaple_utils.dir/logstream.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/utils/logstream.cpp make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/phylo-yaml /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/phylo-yaml /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color=" phyloYAML make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 36%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/phylo-yaml/statespace.cpp [ 36%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 36%] Built target pllavx make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color=" terraphast make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/advanced.cpp [ 36%] Linking CXX static library libcmaple_utils.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/utils && /usr/bin/cmake -P CMakeFiles/cmaple_utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_utils.dir/link.txt --verbose=1 "/usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 36%] Built target cmaple_utils [ 37%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/bigint.cpp make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils/CMakeFiles/decentTree.dir/DependInfo.cmake "--color=" decentTree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f utils/CMakeFiles/decentTree.dir/build.make utils/CMakeFiles/decentTree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 37%] Building CXX object utils/CMakeFiles/decentTree.dir/decenttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/decenttree.cpp.o -MF CMakeFiles/decentTree.dir/decenttree.cpp.o.d -o CMakeFiles/decentTree.dir/decenttree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/decenttree.cpp [ 37%] 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/iqtree3-3.1.1+dfsg/build.mpi' [ 37%] Built target kernelsse [ 37%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/bipartitions.cpp [ 38%] Building CXX object utils/CMakeFiles/decentTree.dir/starttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/starttree.cpp.o -MF CMakeFiles/decentTree.dir/starttree.cpp.o.d -o CMakeFiles/decentTree.dir/starttree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/starttree.cpp [ 38%] 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/iqtree3-3.1.1+dfsg/build.mpi' [ 38%] Built target kernelfma make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" utils make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 40%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/eigendecomposition.cpp [ 40%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj.cpp.o -MF CMakeFiles/decentTree.dir/bionj.cpp.o.d -o CMakeFiles/decentTree.dir/bionj.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/bionj.cpp [ 40%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/bitmatrix.cpp [ 40%] Building CXX object utils/CMakeFiles/decentTree.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/bionj2.cpp.o -MF CMakeFiles/decentTree.dir/bionj2.cpp.o.d -o CMakeFiles/decentTree.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/bionj2.cpp [ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/clamped_uint.cpp [ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/constraints.cpp make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/pda /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pda /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color=" pda make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 41%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/circularnetwork.cpp [ 41%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/gzstream.cpp [ 41%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/optimization.cpp [ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/errors.cpp [ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/multitree.cpp [ 43%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 /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/iqtree3-3.1.1+dfsg/build.mpi' [ 43%] Built target kernelavx [ 44%] Building CXX object utils/CMakeFiles/decentTree.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/gzstream.cpp.o -MF CMakeFiles/decentTree.dir/gzstream.cpp.o.d -o CMakeFiles/decentTree.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/gzstream.cpp [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/multitree_iterator.cpp [ 44%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/greedy.cpp [ 45%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/gurobiwrapper.cpp [ 46%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/stoprule.cpp [ 46%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/nodes.cpp [ 46%] Linking CXX static library libphyloYAML.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 46%] Built target phyloYAML [ 46%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/hashsplitset.cpp [ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/parser.cpp [ 47%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/pdnetwork.cpp [ 48%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/pruning.cpp [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/rooting.cpp [ 48%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/tools.cpp [ 48%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/split.cpp [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/simple.cpp [ 49%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/subtree_extraction.cpp [ 49%] Building CXX object utils/CMakeFiles/decentTree.dir/progress.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/progress.cpp.o -MF CMakeFiles/decentTree.dir/progress.cpp.o.d -o CMakeFiles/decentTree.dir/progress.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/progress.cpp [ 49%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/supertree_helpers.cpp [ 49%] Building CXX object utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT utils/CMakeFiles/decentTree.dir/operatingsystem.cpp.o -MF CMakeFiles/decentTree.dir/operatingsystem.cpp.o.d -o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/operatingsystem.cpp make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/alignment/CMakeFiles/cmaple_alignment.dir/DependInfo.cmake "--color=" cmaple_alignment make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build.make cmaple/alignment/CMakeFiles/cmaple_alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 49%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/alignment && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -MF CMakeFiles/cmaple_alignment.dir/mutation.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/mutation.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/mutation.cpp [ 50%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/alignment && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregion.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/trees.cpp [ 51%] Linking CXX executable decentTree cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/decentTree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/decentTree.dir/link.d CMakeFiles/decentTree.dir/decenttree.cpp.o CMakeFiles/decentTree.dir/starttree.cpp.o CMakeFiles/decentTree.dir/bionj.cpp.o CMakeFiles/decentTree.dir/bionj2.cpp.o CMakeFiles/decentTree.dir/gzstream.cpp.o CMakeFiles/decentTree.dir/progress.cpp.o CMakeFiles/decentTree.dir/operatingsystem.cpp.o -o decentTree -L/build/reproducible-path/iqtree3-3.1.1+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+dfsg/lib /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 51%] Built target decentTree [ 51%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/splitgraph.cpp [ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/union_find.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/splitset.cpp [ 53%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/alignment && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.cpp [ 53%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/pllnni.cpp [ 54%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/checkpoint.cpp [ 54%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/validation.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 54%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/alignment && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o -MF CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.cpp [ 54%] Linking CXX static library libterraphast.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 54%] Built target terraphast [ 55%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/alignment && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -MF CMakeFiles/cmaple_alignment.dir/sequence.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.h:3, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregionsmem.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 55%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/lpwrapper.c [ 55%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/MPIHelper.cpp [ 55%] Building CXX object utils/CMakeFiles/utils.dir/starttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/starttree.cpp.o -MF CMakeFiles/utils.dir/starttree.cpp.o.d -o CMakeFiles/utils.dir/starttree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/starttree.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 56%] Building CXX object utils/CMakeFiles/utils.dir/bionj.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj.cpp.o -MF CMakeFiles/utils.dir/bionj.cpp.o.d -o CMakeFiles/utils.dir/bionj.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/bionj.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o [ 56%] Building CXX object utils/CMakeFiles/utils.dir/bionj2.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/bionj2.cpp.o -MF CMakeFiles/utils.dir/bionj2.cpp.o.d -o CMakeFiles/utils.dir/bionj2.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/bionj2.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/ecopd.cpp [ 56%] Building CXX object cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/alignment && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/alignment/CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -MF CMakeFiles/cmaple_alignment.dir/alignment.cpp.o.d -o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/graph.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/progress.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/progress.cpp.o -MF CMakeFiles/utils.dir/progress.cpp.o.d -o CMakeFiles/utils.dir/progress.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/progress.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/pdtree.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/operatingsystem.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/operatingsystem.cpp.o -MF CMakeFiles/utils.dir/operatingsystem.cpp.o.d -o CMakeFiles/utils.dir/operatingsystem.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/utils/operatingsystem.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/alignment.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 58%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/pdtreeset.cpp [ 58%] Linking CXX static library libcmaple_alignment.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/alignment && /usr/bin/cmake -P CMakeFiles/cmaple_alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_alignment.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-15" qc libcmaple_alignment.a CMakeFiles/cmaple_alignment.dir/mutation.cpp.o CMakeFiles/cmaple_alignment.dir/seqregion.cpp.o CMakeFiles/cmaple_alignment.dir/seqregions.cpp.o CMakeFiles/cmaple_alignment.dir/seqregionsmem.cpp.o CMakeFiles/cmaple_alignment.dir/sequence.cpp.o CMakeFiles/cmaple_alignment.dir/alignment.cpp.o "/usr/bin/gcc-ranlib-15" libcmaple_alignment.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 58%] Built target cmaple_alignment [ 58%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/pda/ecopdmtreeset.cpp make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/model/CMakeFiles/cmaple_model.dir/DependInfo.cmake "--color=" cmaple_model make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f cmaple/model/CMakeFiles/cmaple_model.dir/build.make cmaple/model/CMakeFiles/cmaple_model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 58%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/model && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model.cpp.o -MF CMakeFiles/cmaple_model.dir/model.cpp.o.d -o CMakeFiles/cmaple_model.dir/model.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.cpp [ 58%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/model && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/modelbase.cpp.o -MF CMakeFiles/cmaple_model.dir/modelbase.cpp.o.d -o CMakeFiles/cmaple_model.dir/modelbase.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/modelbase.cpp [ 60%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/model && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_dna.cpp.o -MF CMakeFiles/cmaple_model.dir/model_dna.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_dna.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.cpp [ 61%] Linking CXX static library libpda.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 61%] Built target pda [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/model && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_aa.cpp.o -MF CMakeFiles/cmaple_model.dir/model_aa.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_aa.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.cpp [ 61%] Building CXX object cmaple/model/CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/model/CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o -MF CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o.d -o CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/modelbase.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.h:3, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_dna_rate_variation.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 61%] Linking CXX static library libutils.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 61%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/model /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake "--color=" model make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 61%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o [ 62%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelmarkov.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modeldna.cpp [ 62%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelbin.cpp [ 62%] Building CXX object model/CMakeFiles/model.dir/modeldnaerror.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldnaerror.cpp.o -MF CMakeFiles/model.dir/modeldnaerror.cpp.o.d -o CMakeFiles/model.dir/modeldnaerror.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modeldnaerror.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/model_aa.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/model/../alignment/../model/../utils/matrix.h:34: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:319:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 319 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ [ 62%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelfactory.cpp [ 63%] Linking CXX static library libcmaple_model.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/model && /usr/bin/cmake -P CMakeFiles/cmaple_model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_model.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-15" qc libcmaple_model.a CMakeFiles/cmaple_model.dir/model.cpp.o CMakeFiles/cmaple_model.dir/modelbase.cpp.o CMakeFiles/cmaple_model.dir/model_dna.cpp.o CMakeFiles/cmaple_model.dir/model_aa.cpp.o CMakeFiles/cmaple_model.dir/model_dna_rate_variation.cpp.o "/usr/bin/gcc-ranlib-15" libcmaple_model.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 63%] Built target cmaple_model [ 64%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelprotein.cpp [ 64%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelset.cpp [ 64%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelsubst.cpp make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/tree/CMakeFiles/cmaple_tree.dir/DependInfo.cmake "--color=" cmaple_tree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f cmaple/tree/CMakeFiles/cmaple_tree.dir/build.make cmaple/tree/CMakeFiles/cmaple_tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 64%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/tree && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/tree.cpp.o -MF CMakeFiles/cmaple_tree.dir/tree.cpp.o.d -o CMakeFiles/cmaple_tree.dir/tree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/tree.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/partitionmodel.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/partitionmodelplen.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rategamma.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/tree.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:34: /usr/include/simde/x86/avx.h: In function ‘simde__m256d simde__m256d_from_private(simde__m256d_private)’: /usr/include/simde/x86/avx.h:319:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 319 | simde__m256d_from_private(simde__m256d_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ [ 66%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rategammainvar.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h: In function ‘cmaple::initLhVecMerge<(unsigned short)20>(unsigned short, double, cmaple::ModelBase const*, bool, std::unique_ptr, std::default_delete > > const&)std::array’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1617 | output_lh_vec[i] = equal_prob; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop 1616 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h: In function ‘cmaple::do_merge_ORACGT_ORACGT<(unsigned short)20>(cmaple::SeqRegion const&, cmaple::SeqRegion const&, double, double, double, int, cmaple::Alignment const*, cmaple::ModelBase const*, double, std::unique_ptr >&, bool, double&)bool’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1872:35: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1872 | seq1_lh_vec[i] *= model->root_freqs[i]; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1870:35: note: within this loop 1870 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] 1940 | total_prob += merged_lh_vec[i]; /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop 1939 | for (auto i = 0; i < num_states; ++i) | ~~^~~~~~~~~~~~ [ 66%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgamma.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratecontinuousgamma.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -MF CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o.d -o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratecontinuousgammainvar.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rateheterogeneity.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rateinvar.cpp [ 67%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/tree && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/updatingnode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratemeyerdiscrete.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratemeyerhaeseler.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratekategory.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/updatingnode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 69%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/tree && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -MF CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/traversingnode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratefree.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/ratefreeinvar.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rateheterotachy.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/traversingnode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 70%] Building CXX object cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/tree && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/tree/CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -MF CMakeFiles/cmaple_tree.dir/phylonode.cpp.o.d -o CMakeFiles/cmaple_tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/rateheterotachyinvar.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelcodon.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/internal.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/phylonode.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 71%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelmorphology.cpp [ 71%] Linking CXX static library libcmaple_tree.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/tree && /usr/bin/cmake -P CMakeFiles/cmaple_tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple_tree.dir/link.txt --verbose=1 "/usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 71%] Built target cmaple_tree make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/maple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/maple/CMakeFiles/maple.dir/DependInfo.cmake "--color=" maple make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f cmaple/maple/CMakeFiles/maple.dir/build.make cmaple/maple/CMakeFiles/maple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 71%] Building CXX object cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/maple && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT cmaple/maple/CMakeFiles/maple.dir/cmaple.cpp.o -MF CMakeFiles/maple.dir/cmaple.cpp.o.d -o CMakeFiles/maple.dir/cmaple.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelmixture.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelunrest.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.cpp:1: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 72%] Linking CXX static library libmaple.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/maple && /usr/bin/cmake -P CMakeFiles/maple.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/maple && /usr/bin/cmake -E cmake_link_script CMakeFiles/maple.dir/link.txt --verbose=1 "/usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 72%] Built target maple make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/depend [ 73%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple/CMakeFiles/cmaple.dir/DependInfo.cmake "--color=" cmaple cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelliemarkov.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f cmaple/CMakeFiles/cmaple.dir/build.make cmaple/CMakeFiles/cmaple.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 74%] Building CXX object cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/after -I/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/system -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -std=gnu++20 -flto=auto -fno-fat-lto-objects -I/usr/include/eigen3 -I/usr/include -MD -MT cmaple/CMakeFiles/cmaple.dir/main/main.cpp.o -MF CMakeFiles/cmaple.dir/main/main.cpp.o.d -o CMakeFiles/cmaple.dir/main/main.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/main.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelpomo.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelpomomixture.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/main.cpp:32: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/main/../maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 74%] Linking CXX executable cmaple cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple && /usr/bin/cmake -E cmake_link_script CMakeFiles/cmaple.dir/link.txt --verbose=1 tree/./cmaple/tree/../alignment/../model/../utils/matrix.h: In function ‘mul4’: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:132:22: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] [ 75%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelfactorymixlen.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelhmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmm.cpp.o -MF CMakeFiles/model.dir/modelhmm.cpp.o.d -o CMakeFiles/model.dir/modelhmm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelhmm.cpp In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1793:38, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2137:51: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:1783:8, inlined from ‘merge_notN_notN_TwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at tree/./cmaple/tree/../alignment/seqregions.h:2137:51: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1160:54, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1425:35: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1125:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1425:35: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_RACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1230:51, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1305:34, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1431:39: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1262:8, inlined from ‘mergeUpperLower’ at tree/./cmaple/tree/../alignment/seqregions.h:1431:39: tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: tree/./cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] tree/./cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘initLhVecMerge’ at tree/./cmaple/tree/../alignment/seqregions.h:1589:46: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: tree/./cmaple/tree/../alignment/seqregions.h:535:1: note: destination object ‘output_lh_vec’ of size 32 In function ‘do_merge_ORACGT_ORACGT’, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] tree/./cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:1931:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at tree/./cmaple/tree/../alignment/seqregions.h:2890:44: tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: tree/./cmaple/tree/../alignment/seqregions.h:1826:36: note: destination object ‘seq2_lh_vec’ of size 32 [ 75%] Building CXX object model/CMakeFiles/model.dir/modelhmmgm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmgm.cpp.o -MF CMakeFiles/model.dir/modelhmmgm.cpp.o.d -o CMakeFiles/model.dir/modelhmmgm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelhmmgm.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelhmmtm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelhmmtm.cpp.o -MF CMakeFiles/model.dir/modelhmmtm.cpp.o.d -o CMakeFiles/model.dir/modelhmmtm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelhmmtm.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelcodonmixture.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodonmixture.cpp.o -MF CMakeFiles/model.dir/modelcodonmixture.cpp.o.d -o CMakeFiles/model.dir/modelcodonmixture.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/model/modelcodonmixture.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--dependency-file=CMakeFiles/cmaple.dir/link.d CMakeFiles/cmaple.dir/main/main.cpp.o -o cmaple -L/build/reproducible-path/iqtree3-3.1.1+dfsg/lib -L/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/libraries/static/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+dfsg/lib:/build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/libraries/static/lib maple/libmaple.a tree/libcmaple_tree.a model/libcmaple_model.a ../ncl/libncl.a ../nclextra/libnclextra.a alignment/libcmaple_alignment.a utils/libcmaple_utils.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 76%] Built target cmaple [ 76%] Linking CXX static library libmodel.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modeldnaerror.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/ratecontinuousgamma.cpp.o CMakeFiles/model.dir/ratecontinuousgammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o CMakeFiles/model.dir/modelhmm.cpp.o CMakeFiles/model.dir/modelhmmgm.cpp.o CMakeFiles/model.dir/modelhmmtm.cpp.o CMakeFiles/model.dir/modelcodonmixture.cpp.o /usr/bin/ranlib libmodel.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 76%] Built target model make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/simulator /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/simulator/CMakeFiles/simulator.dir/DependInfo.cmake "--color=" simulator make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f simulator/CMakeFiles/simulator.dir/build.make simulator/CMakeFiles/simulator.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorinvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator/alisimulatorinvar.cpp [ 77%] Building CXX object simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneityinvar.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator/alisimulatorheterogeneityinvar.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/simulator && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o -MF CMakeFiles/simulator.dir/alisimulator.cpp.o.d -o CMakeFiles/simulator.dir/alisimulator.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator/alisimulator.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/simulator && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT simulator/CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -MF CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o.d -o CMakeFiles/simulator.dir/alisimulatorheterogeneity.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/simulator/alisimulatorheterogeneity.cpp [ 78%] Linking CXX static library libsimulator.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/simulator && /usr/bin/cmake -P CMakeFiles/simulator.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/simulator && /usr/bin/cmake -E cmake_link_script CMakeFiles/simulator.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 78%] Built target simulator make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" alignment make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/substitution.cpp.o [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/alignment.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/pattern.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/substitution.cpp.o -MF CMakeFiles/alignment.dir/substitution.cpp.o.d -o CMakeFiles/alignment.dir/substitution.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/substitution.cpp [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o [ 80%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/alignmentpairwise.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentsummary.cpp.o -MF CMakeFiles/alignment.dir/alignmentsummary.cpp.o.d -o CMakeFiles/alignment.dir/alignmentsummary.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/alignmentsummary.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/maalignment.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/superalignment.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/superalignmentpairwise.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/superalignmentpairwiseplen.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/superalignmentunlinked.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/sequence.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequence.cpp.o -MF CMakeFiles/alignment.dir/sequence.cpp.o.d -o CMakeFiles/alignment.dir/sequence.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/sequence.cpp [ 82%] Building CXX object alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -MF CMakeFiles/alignment.dir/sequencechunkstr.cpp.o.d -o CMakeFiles/alignment.dir/sequencechunkstr.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/alignment/sequencechunkstr.cpp [ 83%] Linking CXX static library libalignment.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 83%] Built target alignment make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color=" tree make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 83%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -MF CMakeFiles/tree.dir/iqtreemixhmm.cpp.o.d -o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/iqtreemixhmm.cpp [ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/constrainttree.cpp [ 84%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 84%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/matree.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/iqtree.cpp [ 84%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtreemix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/candidateset.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtreemix.cpp.o -MF CMakeFiles/tree.dir/iqtreemix.cpp.o.d -o CMakeFiles/tree.dir/iqtreemix.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/iqtreemix.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/memslot.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/mexttree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/mtree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/mtreeset.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/ncbitree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/node.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/genomenode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genomenode.cpp.o -MF CMakeFiles/tree.dir/genomenode.cpp.o.d -o CMakeFiles/tree.dir/genomenode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/genomenode.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/genometree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/genometree.cpp.o -MF CMakeFiles/tree.dir/genometree.cpp.o.d -o CMakeFiles/tree.dir/genometree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/genometree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylonode.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylonodemixlen.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosuperhmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosuperhmm.cpp.o -MF CMakeFiles/tree.dir/phylosuperhmm.cpp.o.d -o CMakeFiles/tree.dir/phylosuperhmm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosuperhmm.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosupertree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosupertreeplen.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylosupertreeunlinked.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylotree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylotreemixlen.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylotreepars.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylotreesse.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/quartet.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/supernode.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/tinatree.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/parstree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/discordance.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylohmm.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylohmm.cpp.o -MF CMakeFiles/tree.dir/phylohmm.cpp.o.d -o CMakeFiles/tree.dir/phylohmm.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/tree/phylohmm.cpp [ 93%] Linking CXX static library libtree.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/iqtreemix.cpp.o CMakeFiles/tree.dir/iqtreemixhmm.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/genomenode.cpp.o CMakeFiles/tree.dir/genometree.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosuperhmm.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o CMakeFiles/tree.dir/discordance.cpp.o CMakeFiles/tree.dir/phylohmm.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 93%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terrace /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color=" terrace make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/terracetphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terracetphast /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terracetphast/CMakeFiles/terracetphast.dir/DependInfo.cmake "--color=" terracetphast make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f terracetphast/CMakeFiles/terracetphast.dir/build.make terracetphast/CMakeFiles/terracetphast.dir/build make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracetree.cpp.o [ 95%] Building CXX object terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -MF CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o.d -o CMakeFiles/terrace.dir/presenceabsencematrix.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace/presenceabsencematrix.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terracetphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terracetphast/CMakeFiles/terracetphast.dir/terracetphast.cpp.o -MF CMakeFiles/terracetphast.dir/terracetphast.cpp.o.d -o CMakeFiles/terracetphast.dir/terracetphast.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terracetphast/terracetphast.cpp cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracetree.cpp.o -MF CMakeFiles/terrace.dir/terracetree.cpp.o.d -o CMakeFiles/terrace.dir/terracetree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace/terracetree.cpp [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o [ 95%] Building CXX object terrace/CMakeFiles/terrace.dir/terracenode.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terracenode.cpp.o -MF CMakeFiles/terrace.dir/terracenode.cpp.o.d -o CMakeFiles/terrace.dir/terracenode.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace/terracenode.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/terrace/terrace.cpp [ 95%] Linking CXX static library libterracetphast.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terracetphast && /usr/bin/cmake -P CMakeFiles/terracetphast.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terracetphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terracetphast.dir/link.txt --verbose=1 /usr/bin/ar qc libterracetphast.a CMakeFiles/terracetphast.dir/terracetphast.cpp.o /usr/bin/ranlib libterracetphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 95%] Built target terracetphast [ 95%] Linking CXX static library libterrace.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 95%] Built target terrace make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/main /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/main /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/main/CMakeFiles/main.dir/DependInfo.cmake "--color=" main make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [ 96%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o [ 96%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/main.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/main && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp [ 96%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp [ 97%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o [ 97%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/main && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/timetree.cpp cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/main && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/treetesting.cpp [ 97%] Building CXX object main/CMakeFiles/main.dir/alisim.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/alisim.cpp.o -MF CMakeFiles/main.dir/alisim.cpp.o.d -o CMakeFiles/main.dir/alisim.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/alisim.cpp /build/reproducible-path/iqtree3-3.1.1+dfsg/main/main.cpp:132:25: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 132 | out << " built " << __DATE__; | ^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp:1451:53: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 1451 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/alisim.h:15, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/alisim.cpp:8: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/main.cpp:52: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp: In function ‘char* initFreqSet(PML::SeqType)’: /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6288:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6288 | case SEQ_CODON: return ",F1X4,F3X4"; | ^~~~~~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6289:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6289 | case SEQ_MORPH: return "FQ"; | ^~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6290:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6290 | case SEQ_PROTEIN: return ",FO"; | ^~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:6291:34: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 6291 | default: return "FO"; | ^~~~ In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phylotesting.cpp:42: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 98%] Building CXX object main/CMakeFiles/main.dir/terraceanalysis.cpp.o cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/main && /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/terraceanalysis.cpp.o -MF CMakeFiles/main.dir/terraceanalysis.cpp.o.d -o CMakeFiles/main.dir/terraceanalysis.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/main/terraceanalysis.cpp In file included from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/modelbase.h:8, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/seqregions.h:4, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/sequence.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/alignment.h:2, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/tree.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/cmaple.h:1, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.h:34, from /build/reproducible-path/iqtree3-3.1.1+dfsg/main/phyloanalysis.cpp:32: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h: In instantiation of ‘simde__m256d mul4(const double*, const double*) [with int offsetRegs = 0; simde__m256d = simde__m256d]’: /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:128:22: required from here 128 | auto dot0 = mul4<0>(p1, p2); | ~~~~~~~^~~~~~~~ /build/reproducible-path/iqtree3-3.1.1+dfsg/cmaple/maple/../tree/../alignment/../model/../utils/matrix.h:54:21: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] 54 | inline simde__m256d mul4(const double* p1, const double* p2) | ^~~~ [ 98%] Linking CXX static library libmain.a cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/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/iqtree3-3.1.1+dfsg/build.mpi' [ 98%] Built target main make -f CMakeFiles/iqtree3.dir/build.make CMakeFiles/iqtree3.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' cd /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/CMakeFiles/iqtree3.dir/DependInfo.cmake "--color=" iqtree3 make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make -f CMakeFiles/iqtree3.dir/build.make CMakeFiles/iqtree3.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [100%] Building CXX object CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o /usr/bin/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/iqtree3-3.1.1+dfsg -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi -I/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/cmaple -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/include -I/build/reproducible-path/iqtree3-3.1.1+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o -c /build/reproducible-path/iqtree3-3.1.1+dfsg/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree3-mpi /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree3.dir/link.txt --verbose=1 cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1617:38: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1616:36: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘initLhVecMerge’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1589:46: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In function ‘initLhVecMerge’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:535:1: note: destination object ‘output_lh_vec’ of size 32 cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h: In function ‘mul4’: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:132:22: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi] In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1793:38, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2137:51: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1783:8, inlined from ‘merge_notN_notN_TwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2049:52, inlined from ‘mergeTwoLowers’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2137:51: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1160:54, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1425:35: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_O_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1125:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1425:35: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘merge_RACGT_RACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1230:51, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1305:34, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1431:39: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] In function ‘make_unique’, inlined from ‘merge_RACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1262:8, inlined from ‘mergeUpperLower’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1431:39: cmaple/tree/./cmaple/tree/../alignment/../model/../alignment/../utils/tools.h:1318:29: note: destination object of size 32 allocated by ‘operator new’ In function ‘do_merge_ORACGT_ORACGT’, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1940:20: warning: iteration 4 invokes undefined behavior [-Waggressive-loop-optimizations] cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1939:24: note: within this loop In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1898:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:23: note: destination object ‘seq1_lh_vec’ of size 32 In function ‘resetVec’, inlined from ‘resetLhVecExceptState’ at cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:293:21, inlined from ‘do_merge_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1931:45, inlined from ‘calSiteLhs_ORACGT_ORACGT’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2692:44, inlined from ‘calSiteLhs_notN_notN’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2764:50, inlined from ‘calculateSiteLhContributions’ at cmaple/tree/./cmaple/tree/../alignment/seqregions.h:2890:44: cmaple/tree/./cmaple/tree/../alignment/../model/../utils/matrix.h:286:20: warning: ‘__builtin_memset’ writing 160 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] cmaple/tree/./cmaple/tree/../alignment/seqregions.h: In member function ‘calculateSiteLhContributions’: cmaple/tree/./cmaple/tree/../alignment/seqregions.h:1826:36: note: destination object ‘seq2_lh_vec’ of size 32 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree3-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/lib/x86_64-linux-gnu/openmpi/include/ -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/iqtree3.dir/link.d CMakeFiles/iqtree3.dir/obsolete/parsmultistate.cpp.o -o iqtree3-mpi -L/build/reproducible-path/iqtree3-3.1.1+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree3-3.1.1+dfsg/lib:/usr/lib/x86_64-linux-gnu/openmpi/lib: booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a simulator/libsimulator.a terrace/libterrace.a -lyaml-cpp phylo-yaml/libphyloYAML.a main/libmain.a cmaple/maple/libmaple.a -lm terracetphast/libterracetphast.a lsd2/liblsd2.a libkernelsse.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so pll/libpllavx.a libkernelavx.a libkernelfma.a -lyaml-cpp booster/libbooster.a pda/libpda.a whtest/libwhtest.a vectorclass/libvectorclass.a terrace/libterrace.a cmaple/tree/libcmaple_tree.a cmaple/model/libcmaple_model.a nclextra/libnclextra.a cmaple/alignment/libcmaple_alignment.a cmaple/utils/libcmaple_utils.a tree/libtree.a pll/libpll.a alignment/libalignment.a simulator/libsimulator.a alignment/libalignment.a simulator/libsimulator.a ncl/libncl.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a /usr/lib/x86_64-linux-gnu/libz.so gsl/libgsl.a terraphast/libterraphast.a make[4]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' [100%] Built target iqtree3 make[3]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree3 ] ; then mv build.omp/iqtree3 build.omp/iqtree3-omp ; fi dh override_dh_auto_build make[1]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' # use only the first example for build time test to save time on autobuilders sed '/ myprefix/,$d' debian/Documents_source/example.sh > example.short echo 'time /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/iqtree3-omp -s example.phy -redo' >> example.short time sh example.short Executing tests using /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/iqtree3-omp ... + /bin/time /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/iqtree3-omp -s example.phy IQ-TREE version 3.1.1 for Linux x86 64-bit built Apr 17 2026 Developed by Bui Quang Minh, Thomas Wong, Nhan Ly-Trong, Huaiyan Ren Contributed by Lam-Tung Nguyen, Dominik Schrempf, Chris Bielow, Olga Chernomor, Michael Woodhams, Diep Thi Hoang, Heiko Schmidt Host: sbuild (AVX512, FMA3, 31 GB RAM) Command: /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/iqtree3-omp -s example.phy Seed: 847809 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Mon Apr 20 19:58:34 2026 Kernel: AVX+FMA - 1 threads (4 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 4 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file example.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Constructing alignment: done in 0.00139777 secs using 99.95% CPU 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 4.2827e-05 secs using 98.07% CPU 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) Checking for duplicate sequences: done in 5.4944e-05 secs 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 968 DNA models (sample size: 1998 epsilon: 0.100) ... No. Model -LnL df AIC AICc BIC 1 JC 23662.322 31 47386.644 47387.653 47560.241 2 JC+I 22587.297 32 45238.594 45239.668 45417.791 3 JC+G4 22258.086 32 44580.171 44581.246 44759.368 4 JC+I+G4 22245.545 33 44557.090 44558.233 44741.887 5 JC+R2 22280.896 33 44627.792 44628.935 44812.589 6 JC+R3 22234.529 35 44539.059 44540.343 44735.056 7 JC+R4 22234.316 37 44542.631 44544.066 44749.828 14 JC+I+R2 22253.511 34 44575.021 44576.233 44765.418 15 JC+I+R3 22236.279 36 44544.559 44545.917 44746.155 16 JC+I+R4 22236.047 38 44548.094 44549.607 44760.891 26 JC+I+G4 22245.545 33 44557.090 44558.233 44741.887 28 JC+R3 22234.529 35 44539.059 44540.343 44735.056 48 F81+I+G4 22245.390 33 44556.780 44557.923 44741.577 50 F81+R3 22234.423 35 44538.847 44540.131 44734.843 70 F81+F+I+G4 22019.012 36 44110.023 44111.382 44311.620 72 F81+F+R3 22009.710 38 44095.420 44096.933 44308.216 92 K2P+I+G4 21833.754 34 43735.507 43736.720 43925.904 94 K2P+R3 21823.497 36 43718.994 43720.353 43920.591 114 K2P+I+G4 21833.754 34 43735.507 43736.720 43925.904 116 K2P+R3 21823.497 36 43718.994 43720.353 43920.591 136 HKY+I+G4 21833.723 34 43735.446 43736.658 43925.842 138 HKY+R3 21823.375 36 43718.750 43720.109 43920.347 158 HKY+F+I+G4 21475.608 37 43025.216 43026.651 43232.413 160 HKY+F+R3 21463.044 39 43004.087 43005.680 43222.483 180 TNe+I+G4 21709.208 35 43488.417 43489.701 43684.413 182 TNe+R3 21704.627 37 43483.254 43484.689 43690.451 202 TNe+I+G4 21709.208 35 43488.416 43489.701 43684.413 204 TNe+R3 21704.627 37 43483.254 43484.689 43690.451 224 TN+I+G4 21709.192 35 43488.384 43489.668 43684.380 226 TN+R3 21704.531 37 43483.062 43484.497 43690.258 246 TN+F+I+G4 21360.556 38 42797.113 42798.626 43009.909 248 TN+F+R3 21357.893 40 42795.785 42797.461 43019.781 268 K3P+I+G4 21833.500 35 43737.000 43738.285 43932.997 270 K3P+R3 21823.165 37 43720.329 43721.764 43927.526 290 K3P+I+G4 21833.500 35 43737.000 43738.285 43932.997 292 K3P+R3 21823.165 37 43720.329 43721.764 43927.526 312 K3Pu+I+G4 21833.491 35 43736.982 43738.266 43932.978 314 K3Pu+R3 21823.146 37 43720.291 43721.726 43927.488 334 K3Pu+F+I+G4 21475.268 38 43026.536 43028.049 43239.332 336 K3Pu+F+R3 21462.781 40 43005.561 43007.237 43229.557 356 TPM2+I+G4 21410.054 35 42890.107 42891.392 43086.104 358 TPM2+R3 21403.723 37 42881.446 42882.881 43088.642 378 TPM2+I+G4 21410.054 35 42890.107 42891.392 43086.104 380 TPM2+R3 21403.723 37 42881.446 42882.881 43088.642 400 TPM2u+I+G4 21409.971 35 42889.943 42891.227 43085.939 402 TPM2u+R3 21403.672 37 42881.344 42882.778 43088.540 422 TPM2u+F+I+G4 21291.534 38 42659.067 42660.580 42871.863 424 TPM2u+F+R3 21283.140 40 42646.279 42647.955 42870.275 444 TPM3+I+G4 21833.173 35 43736.345 43737.630 43932.342 446 TPM3+R3 21822.918 37 43719.835 43721.270 43927.032 466 TPM3+I+G4 21833.173 35 43736.345 43737.630 43932.342 468 TPM3+R3 21822.918 37 43719.835 43721.270 43927.032 488 TPM3u+I+G4 21833.165 35 43736.329 43737.614 43932.326 490 TPM3u+R3 21822.895 37 43719.790 43721.225 43926.987 510 TPM3u+F+I+G4 21474.774 38 43025.548 43027.061 43238.344 512 TPM3u+F+R3 21462.249 40 43004.497 43006.173 43228.493 532 TIMe+I+G4 21709.177 36 43490.354 43491.713 43691.951 534 TIMe+R3 21704.568 38 43485.137 43486.650 43697.933 554 TIMe+I+G4 21709.177 36 43490.354 43491.713 43691.951 556 TIMe+R3 21704.568 38 43485.137 43486.650 43697.933 576 TIM+I+G4 21709.159 36 43490.319 43491.677 43691.915 578 TIM+R3 21704.413 38 43484.826 43486.339 43697.623 598 TIM+F+I+G4 21360.250 39 42798.499 42800.093 43016.895 600 TIM+F+R3 21357.475 41 42796.949 42798.710 43026.545 620 TIM2e+I+G4 21309.009 36 42690.017 42691.376 42891.614 622 TIM2e+R3 21303.615 38 42683.230 42684.743 42896.027 642 TIM2e+I+G4 21309.009 36 42690.017 42691.376 42891.614 644 TIM2e+R3 21303.615 38 42683.230 42684.743 42896.027 664 TIM2+I+G4 21308.990 36 42689.980 42691.338 42891.576 666 TIM2+R3 21303.600 38 42683.199 42684.712 42895.995 686 TIM2+F+I+G4 21152.740 39 42383.479 42385.073 42601.876 688 TIM2+F+R3 21150.544 41 42383.088 42384.849 42612.684 708 TIM3e+I+G4 21708.502 36 43489.004 43490.362 43690.600 710 TIM3e+R3 21703.969 38 43483.938 43485.451 43696.734 730 TIM3e+I+G4 21708.502 36 43489.004 43490.362 43690.600 732 TIM3e+R3 21703.969 38 43483.938 43485.451 43696.734 752 TIM3+I+G4 21708.481 36 43488.963 43490.321 43690.559 754 TIM3+R3 21703.960 38 43483.920 43485.433 43696.716 774 TIM3+F+I+G4 21359.498 39 42796.995 42798.589 43015.392 776 TIM3+F+R3 21357.073 41 42796.146 42797.907 43025.742 796 TVMe+I+G4 21407.653 37 42889.307 42890.741 43096.503 798 TVMe+R3 21401.543 39 42881.086 42882.680 43099.483 818 TVMe+I+G4 21407.653 37 42889.307 42890.741 43096.503 820 TVMe+R3 21401.543 39 42881.086 42882.680 43099.483 840 TVM+I+G4 21407.642 37 42889.285 42890.719 43096.481 842 TVM+R3 21401.486 39 42880.972 42882.566 43099.369 862 TVM+F+I+G4 21287.934 40 42655.868 42657.544 42879.864 864 TVM+F+R3 21279.783 42 42643.567 42645.414 42878.762 884 SYM+I+G4 21306.024 38 42688.047 42689.560 42900.843 886 SYM+R3 21300.830 40 42681.660 42683.336 42905.656 906 SYM+I+G4 21306.024 38 42688.047 42689.560 42900.843 908 SYM+R3 21300.830 40 42681.660 42683.336 42905.656 928 GTR+I+G4 21306.021 38 42688.043 42689.556 42900.839 930 GTR+R3 21300.830 40 42681.659 42683.335 42905.655 950 GTR+F+I+G4 21148.957 41 42379.913 42381.674 42609.509 952 GTR+F+R3 21147.067 43 42380.134 42382.071 42620.930 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: 6.744 seconds (0h:0m:6s) Wall-clock time for ModelFinder: 6.782 seconds (0h:0m:6s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... Init pinv, alpha: 0.000, 0.780 / Estimate: 0.000, 0.482 / LogL: -21159.728 Init pinv, alpha: 0.038, 0.780 / Estimate: 0.045, 0.533 / LogL: -21156.817 Init pinv, alpha: 0.076, 0.780 / Estimate: 0.083, 0.590 / LogL: -21154.744 Init pinv, alpha: 0.114, 0.780 / Estimate: 0.119, 0.653 / LogL: -21153.275 Init pinv, alpha: 0.153, 0.780 / Estimate: 0.153, 0.728 / LogL: -21152.557 Init pinv, alpha: 0.191, 0.780 / Estimate: 0.182, 0.803 / LogL: -21152.771 Init pinv, alpha: 0.229, 0.780 / Estimate: 0.185, 0.808 / LogL: -21152.833 Init pinv, alpha: 0.267, 0.780 / Estimate: 0.186, 0.812 / LogL: -21152.859 Init pinv, alpha: 0.305, 0.780 / Estimate: 0.186, 0.813 / LogL: -21152.876 Init pinv, alpha: 0.343, 0.780 / Estimate: 0.187, 0.816 / LogL: -21152.898 Optimal pinv,alpha: 0.153, 0.728 / LogL: -21152.557 Parameters optimization took 1.297 sec Wrote distance file to... Computing ML distances based on estimated model parameters... Calculating distance matrix: done in 0.00153163 secs using 99.7% CPU Computing ML distances took 0.001712 sec (of wall-clock time) 0.001680 sec (of CPU time) Setting up auxiliary I and S matrices: done in 5.1133e-05 secs using 97.78% CPU Constructing RapidNJ tree: done in 5.9946e-05 secs using 100.1% CPU Computing RapidNJ tree took 0.000234 sec (of wall-clock time) 0.000155 sec (of CPU time) Log-likelihood of RapidNJ tree: -21161.716 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.205 second Computing log-likelihood of 98 initial trees ... 0.433 seconds Current best score: -21152.557 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -21152.547 Iteration 10 / LogL: -21152.821 / Time: 0h:0m:9s Iteration 20 / LogL: -21154.720 / Time: 0h:0m:9s Finish initializing candidate tree set (2) Current best tree score: -21152.547 / CPU time: 1.554 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -21152.598 / Time: 0h:0m:10s (0h:0m:8s left) Iteration 40 / LogL: -21152.567 / Time: 0h:0m:10s (0h:0m:6s left) Iteration 50 / LogL: -21152.561 / Time: 0h:0m:11s (0h:0m:4s left) Iteration 60 / LogL: -21152.581 / Time: 0h:0m:12s (0h:0m:3s left) Iteration 70 / LogL: -21152.974 / Time: 0h:0m:12s (0h:0m:2s left) Iteration 80 / LogL: -21152.602 / Time: 0h:0m:13s (0h:0m:1s left) Iteration 90 / LogL: -21157.767 / Time: 0h:0m:13s (0h:0m:0s left) Iteration 100 / LogL: -21152.785 / 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: -21152.547 Optimal log-likelihood: -21152.538 Rate parameters: A-C: 5.58435 A-G: 7.63243 A-T: 5.58435 C-G: 1.00000 C-T: 22.64435 G-T: 1.00000 Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225 Proportion of invariable sites: 0.154 Gamma shape alpha: 0.729 Parameters optimization took 1 rounds (0.019 sec) BEST SCORE FOUND : -21152.538 Total tree length: 4.217 Total number of iterations: 102 CPU time used for tree search: 6.216 sec (0h:0m:6s) Wall-clock time used for tree search: 6.305 sec (0h:0m:6s) Total CPU time used: 14.293 sec (0h:0m:14s) Total wall-clock time used: 14.430 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: Mon Apr 20 19:58:49 2026 14.30user 0.10system 0:14.44elapsed 99%CPU (0avgtext+0avgdata 22236maxresident)k 0inputs+144outputs (0major+3680minor)pagefaults 0swaps + time /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/iqtree3-omp -s example.phy -redo IQ-TREE version 3.1.1 for Linux x86 64-bit built Apr 17 2026 Developed by Bui Quang Minh, Thomas Wong, Nhan Ly-Trong, Huaiyan Ren Contributed by Lam-Tung Nguyen, Dominik Schrempf, Chris Bielow, Olga Chernomor, Michael Woodhams, Diep Thi Hoang, Heiko Schmidt Host: sbuild (AVX512, FMA3, 31 GB RAM) Command: /build/reproducible-path/iqtree3-3.1.1+dfsg/build.omp/iqtree3-omp -s example.phy -redo Seed: 291051 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Mon Apr 20 19:58:49 2026 Kernel: AVX+FMA - 1 threads (4 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 4 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file example.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Constructing alignment: done in 0.0014396 secs using 49.94% CPU 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 4.4671e-05 secs using 49.25% CPU 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) Checking for duplicate sequences: done in 5.5921e-05 secs using 48.28% CPU 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 (0.032 sec) Time for fast ML tree search: 0.314 seconds NOTE: ModelFinder requires 6 MB RAM! ModelFinder will test up to 968 DNA models (sample size: 1998 epsilon: 0.100) ... No. Model -LnL df AIC AICc BIC 1 JC 23662.322 31 47386.644 47387.653 47560.241 2 JC+I 22587.297 32 45238.594 45239.668 45417.791 3 JC+G4 22258.086 32 44580.171 44581.246 44759.368 4 JC+I+G4 22245.545 33 44557.090 44558.233 44741.887 5 JC+R2 22280.896 33 44627.792 44628.935 44812.589 6 JC+R3 22234.529 35 44539.059 44540.343 44735.056 7 JC+R4 22234.316 37 44542.631 44544.066 44749.828 14 JC+I+R2 22253.511 34 44575.021 44576.233 44765.418 15 JC+I+R3 22236.279 36 44544.559 44545.917 44746.155 16 JC+I+R4 22236.047 38 44548.094 44549.607 44760.891 26 JC+I+G4 22245.545 33 44557.090 44558.233 44741.887 28 JC+R3 22234.529 35 44539.059 44540.343 44735.056 48 F81+I+G4 22245.390 33 44556.780 44557.923 44741.577 50 F81+R3 22234.423 35 44538.847 44540.131 44734.843 70 F81+F+I+G4 22019.012 36 44110.023 44111.382 44311.620 72 F81+F+R3 22009.710 38 44095.420 44096.933 44308.216 92 K2P+I+G4 21833.754 34 43735.507 43736.720 43925.904 94 K2P+R3 21823.497 36 43718.994 43720.353 43920.591 114 K2P+I+G4 21833.754 34 43735.507 43736.720 43925.904 116 K2P+R3 21823.497 36 43718.994 43720.353 43920.591 136 HKY+I+G4 21833.723 34 43735.446 43736.658 43925.842 138 HKY+R3 21823.375 36 43718.750 43720.109 43920.347 158 HKY+F+I+G4 21475.608 37 43025.216 43026.651 43232.413 160 HKY+F+R3 21463.044 39 43004.087 43005.680 43222.483 180 TNe+I+G4 21709.208 35 43488.417 43489.701 43684.413 182 TNe+R3 21704.627 37 43483.254 43484.689 43690.451 202 TNe+I+G4 21709.208 35 43488.416 43489.701 43684.413 204 TNe+R3 21704.627 37 43483.254 43484.689 43690.451 224 TN+I+G4 21709.192 35 43488.384 43489.668 43684.380 226 TN+R3 21704.531 37 43483.062 43484.497 43690.258 246 TN+F+I+G4 21360.556 38 42797.113 42798.626 43009.909 248 TN+F+R3 21357.893 40 42795.785 42797.461 43019.781 268 K3P+I+G4 21833.500 35 43737.000 43738.285 43932.997 270 K3P+R3 21823.165 37 43720.329 43721.764 43927.526 290 K3P+I+G4 21833.500 35 43737.000 43738.285 43932.997 292 K3P+R3 21823.165 37 43720.329 43721.764 43927.526 312 K3Pu+I+G4 21833.491 35 43736.982 43738.266 43932.978 314 K3Pu+R3 21823.146 37 43720.291 43721.726 43927.488 334 K3Pu+F+I+G4 21475.268 38 43026.536 43028.049 43239.332 336 K3Pu+F+R3 21462.781 40 43005.561 43007.237 43229.557 356 TPM2+I+G4 21410.054 35 42890.107 42891.392 43086.104 358 TPM2+R3 21403.723 37 42881.446 42882.881 43088.642 378 TPM2+I+G4 21410.054 35 42890.107 42891.392 43086.104 380 TPM2+R3 21403.723 37 42881.446 42882.881 43088.642 400 TPM2u+I+G4 21409.971 35 42889.943 42891.227 43085.939 402 TPM2u+R3 21403.672 37 42881.344 42882.778 43088.540 422 TPM2u+F+I+G4 21291.534 38 42659.067 42660.580 42871.863 424 TPM2u+F+R3 21283.140 40 42646.279 42647.955 42870.275 444 TPM3+I+G4 21833.173 35 43736.345 43737.630 43932.342 446 TPM3+R3 21822.918 37 43719.835 43721.270 43927.032 466 TPM3+I+G4 21833.173 35 43736.345 43737.630 43932.342 468 TPM3+R3 21822.918 37 43719.835 43721.270 43927.032 488 TPM3u+I+G4 21833.165 35 43736.329 43737.614 43932.326 490 TPM3u+R3 21822.895 37 43719.790 43721.225 43926.987 510 TPM3u+F+I+G4 21474.774 38 43025.548 43027.061 43238.344 512 TPM3u+F+R3 21462.249 40 43004.497 43006.173 43228.493 532 TIMe+I+G4 21709.177 36 43490.354 43491.713 43691.951 534 TIMe+R3 21704.568 38 43485.137 43486.650 43697.933 554 TIMe+I+G4 21709.177 36 43490.354 43491.713 43691.951 556 TIMe+R3 21704.568 38 43485.137 43486.650 43697.933 576 TIM+I+G4 21709.159 36 43490.319 43491.677 43691.915 578 TIM+R3 21704.413 38 43484.826 43486.339 43697.623 598 TIM+F+I+G4 21360.250 39 42798.499 42800.093 43016.895 600 TIM+F+R3 21357.475 41 42796.949 42798.710 43026.545 620 TIM2e+I+G4 21309.009 36 42690.017 42691.376 42891.614 622 TIM2e+R3 21303.615 38 42683.230 42684.743 42896.027 642 TIM2e+I+G4 21309.009 36 42690.017 42691.376 42891.614 644 TIM2e+R3 21303.615 38 42683.230 42684.743 42896.027 664 TIM2+I+G4 21308.990 36 42689.980 42691.338 42891.576 666 TIM2+R3 21303.600 38 42683.199 42684.712 42895.995 686 TIM2+F+I+G4 21152.740 39 42383.479 42385.073 42601.876 688 TIM2+F+R3 21150.544 41 42383.088 42384.849 42612.684 708 TIM3e+I+G4 21708.502 36 43489.004 43490.362 43690.600 710 TIM3e+R3 21703.969 38 43483.938 43485.451 43696.734 730 TIM3e+I+G4 21708.502 36 43489.004 43490.362 43690.600 732 TIM3e+R3 21703.969 38 43483.938 43485.451 43696.734 752 TIM3+I+G4 21708.481 36 43488.963 43490.321 43690.559 754 TIM3+R3 21703.960 38 43483.920 43485.433 43696.716 774 TIM3+F+I+G4 21359.498 39 42796.995 42798.589 43015.392 776 TIM3+F+R3 21357.073 41 42796.146 42797.907 43025.742 796 TVMe+I+G4 21407.653 37 42889.307 42890.741 43096.503 798 TVMe+R3 21401.543 39 42881.086 42882.680 43099.483 818 TVMe+I+G4 21407.653 37 42889.307 42890.741 43096.503 820 TVMe+R3 21401.543 39 42881.086 42882.680 43099.483 840 TVM+I+G4 21407.642 37 42889.285 42890.719 43096.481 842 TVM+R3 21401.486 39 42880.972 42882.566 43099.369 862 TVM+F+I+G4 21287.934 40 42655.868 42657.544 42879.864 864 TVM+F+R3 21279.783 42 42643.567 42645.414 42878.762 884 SYM+I+G4 21306.024 38 42688.047 42689.560 42900.843 886 SYM+R3 21300.830 40 42681.660 42683.336 42905.656 906 SYM+I+G4 21306.024 38 42688.047 42689.560 42900.843 908 SYM+R3 21300.830 40 42681.660 42683.336 42905.656 928 GTR+I+G4 21306.021 38 42688.043 42689.556 42900.839 930 GTR+R3 21300.830 40 42681.659 42683.335 42905.655 950 GTR+F+I+G4 21148.957 41 42379.913 42381.674 42609.509 952 GTR+F+R3 21147.067 43 42380.134 42382.071 42620.930 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: 6.695 seconds (0h:0m:6s) Wall-clock time for ModelFinder: 6.754 seconds (0h:0m:6s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... Init pinv, alpha: 0.000, 0.780 / Estimate: 0.000, 0.482 / LogL: -21159.728 Init pinv, alpha: 0.038, 0.780 / Estimate: 0.045, 0.533 / LogL: -21156.817 Init pinv, alpha: 0.076, 0.780 / Estimate: 0.083, 0.590 / LogL: -21154.744 Init pinv, alpha: 0.114, 0.780 / Estimate: 0.119, 0.653 / LogL: -21153.275 Init pinv, alpha: 0.153, 0.780 / Estimate: 0.153, 0.728 / LogL: -21152.557 Init pinv, alpha: 0.191, 0.780 / Estimate: 0.182, 0.803 / LogL: -21152.771 Init pinv, alpha: 0.229, 0.780 / Estimate: 0.185, 0.808 / LogL: -21152.833 Init pinv, alpha: 0.267, 0.780 / Estimate: 0.186, 0.812 / LogL: -21152.859 Init pinv, alpha: 0.305, 0.780 / Estimate: 0.186, 0.813 / LogL: -21152.876 Init pinv, alpha: 0.343, 0.780 / Estimate: 0.187, 0.816 / LogL: -21152.898 Optimal pinv,alpha: 0.153, 0.728 / LogL: -21152.557 Parameters optimization took 1.294 sec Wrote distance file to... Computing ML distances based on estimated model parameters... Calculating distance matrix: done in 0.00156566 secs Computing ML distances took 0.001729 sec (of wall-clock time) 0.000120 sec (of CPU time) Setting up auxiliary I and S matrices: done in 4.5083e-05 secs Constructing RapidNJ tree: done in 5.9301e-05 secs Computing RapidNJ tree took 0.000195 sec (of wall-clock time) 0.000000 sec (of CPU time) Log-likelihood of RapidNJ tree: -21161.716 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.196 second Computing log-likelihood of 97 initial trees ... 0.424 seconds Current best score: -21152.557 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -21152.547 Iteration 10 / LogL: -21160.948 / Time: 0h:0m:9s Iteration 20 / LogL: -21152.814 / Time: 0h:0m:9s Finish initializing candidate tree set (2) Current best tree score: -21152.547 / CPU time: 1.595 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -21152.621 / Time: 0h:0m:10s (0h:0m:8s left) Iteration 40 / LogL: -21153.336 / Time: 0h:0m:10s (0h:0m:6s left) Iteration 50 / LogL: -21157.760 / Time: 0h:0m:11s (0h:0m:4s left) Iteration 60 / LogL: -21153.183 / Time: 0h:0m:12s (0h:0m:3s left) Iteration 70 / LogL: -21158.299 / Time: 0h:0m:12s (0h:0m:2s left) Iteration 80 / LogL: -21152.583 / Time: 0h:0m:13s (0h:0m:1s left) Iteration 90 / LogL: -21158.404 / Time: 0h:0m:13s (0h:0m:0s left) Iteration 100 / LogL: -21152.690 / 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: -21152.547 Optimal log-likelihood: -21152.538 Rate parameters: A-C: 5.58435 A-G: 7.63243 A-T: 5.58435 C-G: 1.00000 C-T: 22.64435 G-T: 1.00000 Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225 Proportion of invariable sites: 0.154 Gamma shape alpha: 0.729 Parameters optimization took 1 rounds (0.018 sec) BEST SCORE FOUND : -21152.538 Total tree length: 4.217 Total number of iterations: 102 CPU time used for tree search: 6.262 sec (0h:0m:6s) Wall-clock time used for tree search: 6.337 sec (0h:0m:6s) Total CPU time used: 14.286 sec (0h:0m:14s) Total wall-clock time used: 14.431 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: Mon Apr 20 19:59:03 2026 14.29user 0.12system 0:14.44elapsed 99%CPU (0avgtext+0avgdata 20276maxresident)k 0inputs+144outputs (0major+2657minor)pagefaults 0swaps + rm -rf /tmp/iqtree3-test.Zx4Nd3 28.61user 0.24system 0:28.92elapsed 99%CPU (0avgtext+0avgdata 22236maxresident)k 0inputs+368outputs (0major+8051minor)pagefaults 0swaps rm example.short make[1]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' if [ "omp" != "omp" ] ; then dh_auto_install -Bbuild.omp; fi if [ "serial" != "omp" ] ; then dh_auto_install -Bbuild.serial; fi cd build.serial && make -j6 install DESTDIR=/build/reproducible-path/iqtree3-3.1.1\+dfsg/debian/iqtree3 AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' /usr/bin/cmake -S/build/reproducible-path/iqtree3-3.1.1+dfsg -B/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/bin/iqtree3 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/bin/iqtree3" to "" -- Installing: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./models.nex -- Installing: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./example.phy -- Installing: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./example.nex -- Installing: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./example.cf make[2]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.serial' if [ "mpi" != "omp" ] ; then dh_auto_install -Bbuild.mpi; fi cd build.mpi && make -j6 install DESTDIR=/build/reproducible-path/iqtree3-3.1.1\+dfsg/debian/iqtree3 AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' /usr/bin/cmake -S/build/reproducible-path/iqtree3-3.1.1+dfsg -B/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/bin/iqtree3-mpi -- Set non-toolchain portion of runtime path of "/build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/bin/iqtree3-mpi" to "" -- Up-to-date: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./models.nex -- Up-to-date: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./example.phy -- Up-to-date: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./example.nex -- Up-to-date: /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/./example.cf make[2]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg/build.mpi' dh override_dh_auto_install make[1]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' dh_install find debian -name iqtree3-mpi -exec chrpath --delete \{\} \; find debian -name iqtree3-omp -exec chrpath --delete \{\} \; make[1]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' # somehow the example config is installed in /usr by cmake find debian/iqtree3 -name example.cf -delete dh_installexamples # remove example files in unusual dir rm -f debian/*/usr/models.nex rm -f debian/*/usr/example.[np][eh][xy] make[1]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' mkdir -p /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/share/man/man1/ help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood' \ --version-string="3.1.1+dfsg" /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/bin/iqtree3 > /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/share/man/man1//iqtree3.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="3.1.1+dfsg" /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/bin/iqtree3-omp > /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/share/man/man1//iqtree3-omp.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="3.1.1+dfsg" /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/bin/iqtree3-mpi > /build/reproducible-path/iqtree3-3.1.1+dfsg/debian/iqtree3/usr/share/man/man1//iqtree3-mpi.1 make[1]: Leaving directory '/build/reproducible-path/iqtree3-3.1.1+dfsg' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'iqtree3-dbgsym' in '../iqtree3-dbgsym_3.1.1+dfsg-1_amd64.deb'. dpkg-deb: building package 'iqtree3' in '../iqtree3_3.1.1+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any -O../iqtree3_3.1.1+dfsg-1_amd64.buildinfo dpkg-genchanges --build=any -O../iqtree3_3.1.1+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 2026-04-20T20:01:02Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 20 Apr 2026 20:01:02 +0000 | +------------------------------------------------------------------------------+ iqtree3_3.1.1+dfsg-1_amd64.changes: ----------------------------------- Format: 1.8 Date: Fri, 17 Apr 2026 10:33:24 +0200 Source: iqtree3 Binary: iqtree3 iqtree3-dbgsym Architecture: amd64 Version: 3.1.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: iqtree3 - efficient phylogenetic software by maximum likelihood; v3 Changes: iqtree3 (3.1.1+dfsg-1) unstable; urgency=medium . * Team upload. * d/control: trim trailing whitespace * New upstream version * Remove trailing whitespace in debian/copyright (routine-update) * Refreshed patches. * Reorder Files paragraphs in debian/copyright by directory depth. Checksums-Sha1: 02c33033be9f210d6befd1292849b0c6d4d2ae7f 122161352 iqtree3-dbgsym_3.1.1+dfsg-1_amd64.deb 5308a62713af96a8e88298800832f68dc1bc892d 8745 iqtree3_3.1.1+dfsg-1_amd64.buildinfo 415c31e7f291b931946c1a99cccd0c5b6d05b4b0 10727844 iqtree3_3.1.1+dfsg-1_amd64.deb Checksums-Sha256: dfefd2d26dd5662a125cbd6f9e015610f46208777ed8d66a286c5dbfe11b0d45 122161352 iqtree3-dbgsym_3.1.1+dfsg-1_amd64.deb 8cd0785e40256defaacbf557d21e759b1df9cf72a93b88a0249e65b1f660f694 8745 iqtree3_3.1.1+dfsg-1_amd64.buildinfo c75616ef07a0927ecc7e778448a8a2a32b06e96cff3fb2ad2bcbd4b1e49211fd 10727844 iqtree3_3.1.1+dfsg-1_amd64.deb Files: f47d453d3548923462d2f76b02a8ccfa 122161352 debug optional iqtree3-dbgsym_3.1.1+dfsg-1_amd64.deb ec722340eca338e11f97d43e02614b49 8745 science optional iqtree3_3.1.1+dfsg-1_amd64.buildinfo c129d6bbfed156ea77a400a260a4576d 10727844 science optional iqtree3_3.1.1+dfsg-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Mon, 20 Apr 2026 20:01:03 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: iqtree3 Binary: iqtree3 iqtree3-dbgsym Architecture: amd64 Version: 3.1.1+dfsg-1 Checksums-Md5: f47d453d3548923462d2f76b02a8ccfa 122161352 iqtree3-dbgsym_3.1.1+dfsg-1_amd64.deb c129d6bbfed156ea77a400a260a4576d 10727844 iqtree3_3.1.1+dfsg-1_amd64.deb Checksums-Sha1: 02c33033be9f210d6befd1292849b0c6d4d2ae7f 122161352 iqtree3-dbgsym_3.1.1+dfsg-1_amd64.deb 415c31e7f291b931946c1a99cccd0c5b6d05b4b0 10727844 iqtree3_3.1.1+dfsg-1_amd64.deb Checksums-Sha256: dfefd2d26dd5662a125cbd6f9e015610f46208777ed8d66a286c5dbfe11b0d45 122161352 iqtree3-dbgsym_3.1.1+dfsg-1_amd64.deb c75616ef07a0927ecc7e778448a8a2a32b06e96cff3fb2ad2bcbd4b1e49211fd 10727844 iqtree3_3.1.1+dfsg-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 20 Apr 2026 20:01:00 +0000 Build-Path: /build/reproducible-path/iqtree3-3.1.1+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 (= 1.90.0.2), 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+b1), libctf-nobfd0 (= 2.46-3), libctf0 (= 2.46-3), libcurl4t64 (= 8.20.0~rc2-1), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), 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 (= 1.17.0-1), 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), libgomp1 (= 16-20260322-1), libgprofng0 (= 2.46-3), libgssapi-krb5-2 (= 1.22.1-2+b1), 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 (= 2.5.4-11), libltdl7 (= 2.5.4-11), liblz4-1 (= 1.10.0-9), 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), libncl-dev (= 2.1.21+git20210811.b1213a7-6+b1), libncl2 (= 2.1.21+git20210811.b1213a7-6+b1), libncursesw6 (= 6.6+20251231-1), libnettle8t64 (= 3.10.2-1+b1), 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), 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+b1), 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), 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 (= 3.6.2-1), libstdc++-15-dev (= 15.2.0-16), libstdc++6 (= 16-20260322-1), libsystemd-shared (= 260.1-1), libsystemd0 (= 260.1-1), libtinfo6 (= 6.6+20251231-1), libtool (= 2.5.4-11), libtsan2 (= 16-20260322-1), libubsan1 (= 16-20260322-1), libucc1 (= 1.7.0~rc1-1), libuchardet0 (= 0.0.8-2+b1), libucx0 (= 1.20.1~rc2-1), 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 (= 6.19.12-1), 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 (= 1:10.3p1-1), openssl-provider-legacy (= 3.6.2-1), passwd (= 1:4.19.3-2), patch (= 2.8-2), perl (= 5.40.1-7+b1), perl-base (= 5.40.1-7+b1), 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="1776414804" +------------------------------------------------------------------------------+ | Package contents Mon, 20 Apr 2026 20:01:03 +0000 | +------------------------------------------------------------------------------+ iqtree3-dbgsym_3.1.1+dfsg-1_amd64.deb ------------------------------------- new Debian package, version 2.0. size 122161352 bytes: control archive=700 bytes. 465 bytes, 12 lines control 402 bytes, 4 lines md5sums Package: iqtree3-dbgsym Source: iqtree3 Version: 3.1.1+dfsg-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 129267 Depends: iqtree3 (= 3.1.1+dfsg-1) Section: debug Priority: optional Description: debug symbols for iqtree3 Build-Ids: 46da0d206897244fa7cecd16210fbabf0f6c974e 935d6f9b5bc8192710b8963f28fd011a3d1a6c46 bdc6d3df4dc3f206c30b9283f7890999533b9bd2 drwxr-xr-x root/root 0 2026-04-17 08:33 ./ drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/ drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/lib/ drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/lib/debug/.build-id/46/ -rw-r--r-- root/root 38663584 2026-04-17 08:33 ./usr/lib/debug/.build-id/46/da0d206897244fa7cecd16210fbabf0f6c974e.debug drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/lib/debug/.build-id/93/ -rw-r--r-- root/root 38260016 2026-04-17 08:33 ./usr/lib/debug/.build-id/93/5d6f9b5bc8192710b8963f28fd011a3d1a6c46.debug drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/lib/debug/.build-id/bd/ -rw-r--r-- root/root 38259920 2026-04-17 08:33 ./usr/lib/debug/.build-id/bd/c6d3df4dc3f206c30b9283f7890999533b9bd2.debug drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 17169144 2026-04-17 08:33 ./usr/lib/debug/.dwz/x86_64-linux-gnu/iqtree3.debug drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/share/ drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-04-17 08:33 ./usr/share/doc/iqtree3-dbgsym -> iqtree3 iqtree3_3.1.1+dfsg-1_amd64.deb ------------------------------ new Debian package, version 2.0. size 10727844 bytes: control archive=2352 bytes. 3212 bytes, 60 lines control 1114 bytes, 16 lines md5sums Package: iqtree3 Version: 3.1.1+dfsg-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 36238 Depends: libc6 (>= 2.38), libgcc-s1 (>= 4.0), libgomp1 (>= 6), libopenmpi40 (>= 5.0.10), libstdc++6 (>= 14), libyaml-cpp0.8 (>= 0.7.0), zlib1g (>= 1:1.2.6) Section: science Priority: optional Homepage: http://www.iqtree.org Description: efficient phylogenetic software by maximum likelihood; v3 The IQ-TREE software was created as the successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid accumulation of phylogenomic data, leading to a need for efficient phylogenomic software that can handle a large amount of data and provide more complex models of sequence evolution. To this end, IQ-TREE can utilize multicore computers and distributed parallel computing to speed up the analysis. IQ-TREE automatically performs checkpointing to resume an interrupted analysis. . As input IQ-TREE accepts all common sequence alignment formats including PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable report file (name suffix .iqtree), a NEWICK tree file (.treefile) which can be visualized by tree viewer programs such as FigTree, Dendroscope or iTOL. . Key features of IQ-TREE . - Efficient search algorithm: Fast and effective stochastic algorithm to reconstruct phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihood while requiring similar amount of computing time (Nguyen et al., 2015). - Ultrafast bootstrap: An ultrafast bootstrap approximation (UFBoot) to assess branch supports. UFBoot is 10 to 40 times faster than RAxML rapid bootstrap and obtains less biased support values (Minh et al., 2013). - Accurate model selection: An ultrafast and automatic model selection (ModelFinder) which is 10 to 100 times faster than jModelTest and ProtTest. ModelFinder also finds best-fit partitioning scheme like PartitionFinder (Kalyaanamoorthy et al., 2017). - Alignment simulation: A flexible simulator (AliSim) which allows to simulate sequence alignments under more realistic models than Seq-Gen and INDELible (Ly-Trong et al., 2023). - Phylogenetic testing: Several fast branch tests like SH-aLRT and aBayes test (Anisimova et al., 2011) and tree topology tests like the approximately unbiased (AU) test (Shimodaira, 2002). . The strength of IQ-TREE is the availability of a wide variety of phylogenetic models: . - Common models: All common substitution models for DNA, protein, codon, binary and morphological data with rate heterogeneity among sites and ascertainment bias correction for e.g. SNP data. - Partition models: Allowing individual models for different genomic loci (e.g. genes or codon positions), mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths between partitions. - Mixture Models: fully customizable mixture models and empirical protein mixture models and. - Polymorphism-aware models (PoMo) http://www.iqtree.org/doc/Polymorphism-Aware-Models drwxr-xr-x root/root 0 2026-04-17 08:33 ./ drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/ drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/bin/ -rwxr-xr-x root/root 11521368 2026-04-17 08:33 ./usr/bin/iqtree3 -rwxr-xr-x root/root 11615576 2026-04-17 08:33 ./usr/bin/iqtree3-mpi -rwxr-xr-x root/root 11521368 2026-04-17 08:33 ./usr/bin/iqtree3-omp drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/share/ drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/share/doc/iqtree3/ -rw-r--r-- root/root 278 2026-04-17 08:24 ./usr/share/doc/iqtree3/README.test -rw-r--r-- root/root 905 2026-04-17 08:33 ./usr/share/doc/iqtree3/changelog.Debian.gz -rw-r--r-- root/root 9858 2026-04-17 08:33 ./usr/share/doc/iqtree3/copyright drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/share/doc/iqtree3/examples/ -rw-r--r-- root/root 939 2026-04-02 04:03 ./usr/share/doc/iqtree3/examples/custom_distributions.txt -rw-r--r-- root/root 2237314 2026-04-02 04:03 ./usr/share/doc/iqtree3/examples/example.cf -rw-r--r-- root/root 174 2026-04-02 04:03 ./usr/share/doc/iqtree3/examples/example.nex -rw-r--r-- root/root 34178 2026-04-02 04:03 ./usr/share/doc/iqtree3/examples/example.phy -rw-r--r-- root/root 121669 2026-04-02 04:03 ./usr/share/doc/iqtree3/examples/models.nex -rw-r--r-- root/root 47 2026-04-02 04:03 ./usr/share/doc/iqtree3/examples/tree.nwk -rw-r--r-- root/root 2371 2026-04-17 08:24 ./usr/share/doc/iqtree3/run-unit-test drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/share/man/ drwxr-xr-x root/root 0 2026-04-17 08:33 ./usr/share/man/man1/ -rw-r--r-- root/root 7276 2026-04-17 08:33 ./usr/share/man/man1/iqtree3-mpi.1.gz -rw-r--r-- root/root 7274 2026-04-17 08:33 ./usr/share/man/man1/iqtree3-omp.1.gz -rw-r--r-- root/root 7254 2026-04-17 08:33 ./usr/share/man/man1/iqtree3.1.gz +------------------------------------------------------------------------------+ | Post Build Mon, 20 Apr 2026 20:01:05 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 20 Apr 2026 20:01:05 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 20 Apr 2026 20:01:07 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 3518924 Build-Time: 951 Distribution: unstable Host Architecture: amd64 Install-Time: 3 Job: /srv/rebuilderd/tmp/rebuilderdxJKJah/inputs/iqtree3_3.1.1+dfsg-1.dsc Machine Architecture: amd64 Package: iqtree3 Package-Time: 963 Source-Version: 3.1.1+dfsg-1 Space: 3518924 Status: successful Version: 3.1.1+dfsg-1 -------------------------------------------------------------------------------- Finished at 2026-04-20T20:01:02Z Build needed 00:16:03, 3518924k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderdxJKJah/out checking iqtree3-dbgsym_3.1.1+dfsg-1_amd64.deb: size differs for iqtree3-dbgsym_3.1.1+dfsg-1_amd64.deb