=============================================================================== 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/rebuilderd6UeE2X/inputs/vg_1.59.0+ds-0.1_arm64.buildinfo Source: vg Version: 1.59.0+ds-0.1 rebuilderd-worker node: codethink02-arm64 +------------------------------------------------------------------------------+ | Downloading sources Thu, 27 Nov 2025 13:00:12 +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 [57.5 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 [176 kB] Get:8 https://deb.debian.org/debian experimental InRelease [82.8 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 [6548 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 [94.2 kB] Get:13 https://deb.debian.org/debian trixie-updates/main Sources [2788 B] Get:14 https://deb.debian.org/debian trixie-proposed-updates/main Sources [35.8 kB] Get:15 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [1032 B] Get:16 https://deb.debian.org/debian trixie-backports/main Sources [104 kB] Get:17 https://deb.debian.org/debian forky/non-free-firmware Sources [7408 B] Get:18 https://deb.debian.org/debian forky/main Sources [10.7 MB] Get:19 https://deb.debian.org/debian sid/main Sources [11.2 MB] Get:20 https://deb.debian.org/debian sid/non-free-firmware Sources [9388 B] Get:21 https://deb.debian.org/debian experimental/main Sources [371 kB] Get:22 https://deb.debian.org/debian experimental/non-free-firmware Sources [3332 B] Fetched 33.8 MB in 31s (1090 kB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/v/vg/vg_1.59.0%2bds-0.1.dsc' vg_1.59.0+ds-0.1.dsc 2839 SHA256:d45a8069a8e029b6231deda426707ee3a937447ff090b2197338aa430e1b3b03 'https://deb.debian.org/debian/pool/main/v/vg/vg_1.59.0%2bds.orig.tar.xz' vg_1.59.0+ds.orig.tar.xz 69705744 SHA256:17e43b91bce35905caf9af98e3b839eeff296af7105c1df818eb81004e6ab144 'https://deb.debian.org/debian/pool/main/v/vg/vg_1.59.0%2bds-0.1.debian.tar.xz' vg_1.59.0+ds-0.1.debian.tar.xz 117112 SHA256:dfd2b9a5f833d45b9b5632b651de59668380352bc87fa2654b2c2c7acf6c423b 17e43b91bce35905caf9af98e3b839eeff296af7105c1df818eb81004e6ab144 vg_1.59.0+ds.orig.tar.xz dfd2b9a5f833d45b9b5632b651de59668380352bc87fa2654b2c2c7acf6c423b vg_1.59.0+ds-0.1.debian.tar.xz d45a8069a8e029b6231deda426707ee3a937447ff090b2197338aa430e1b3b03 vg_1.59.0+ds-0.1.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Thu, 27 Nov 2025 13:00:46 +0000 | +------------------------------------------------------------------------------+ Rebuilding vg=1.59.0+ds-0.1 in /srv/rebuilderd/tmp/rebuilderd6UeE2X/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderd6UeE2X/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderd6UeE2X/inputs/vg_1.59.0+ds-0.1_arm64.buildinfo /srv/rebuilderd/tmp/rebuilderd6UeE2X/inputs/vg_1.59.0+ds-0.1_arm64.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/vg-1.59.0+ds I: verifying dsc... successful! Get:1 http://deb.debian.org/debian unstable InRelease [176 kB] Get:2 http://snapshot.debian.org/archive/debian/20241122T143055Z sid InRelease [202 kB] Get:3 http://snapshot.debian.org/archive/debian/20241208T204421Z sid InRelease [202 kB] Get:4 http://deb.debian.org/debian unstable/main arm64 Packages [10.2 MB] Get:5 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 Packages [9955 kB] Get:6 http://snapshot.debian.org/archive/debian/20241208T204421Z sid/main arm64 Packages [9973 kB] Fetched 30.7 MB in 3s (11.1 MB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20241122T143055Z/dists/sid/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted W: http://snapshot.debian.org/archive/debian/20241208T204421Z/dists/sid/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Fetched 127 kB in 0s (6915 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbfbjcook/libidn2-0_2.3.7-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 native-architecture all 0.2.3 [2108 B] Fetched 2108 B in 0s (107 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwcqntmgx/native-architecture_0.2.3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-cran-littler arm64 0.3.20-1+b1 [103 kB] Fetched 103 kB in 0s (5857 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpml9k27rk/r-cran-littler_0.3.20-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 ca-certificates all 20240203 [158 kB] Fetched 158 kB in 0s (8828 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph4udh931/ca-certificates_20240203_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB] Fetched 312 kB in 0s (16.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprxee0cwz/liblzma-dev_5.6.3-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libvcflib-tools arm64 1.0.9+dfsg1-3+b2 [590 kB] Fetched 590 kB in 0s (27.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeoo0tl52/libvcflib-tools_1.0.9+dfsg1-3+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libcairo-gobject2 arm64 1.18.2-2 [130 kB] Fetched 130 kB in 0s (7104 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuc71ycc1/libcairo-gobject2_1.18.2-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libselinux1 arm64 3.7-3+b1 [72.1 kB] Fetched 72.1 kB in 0s (4224 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe4pj57cn/libselinux1_3.7-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 uuid-dev arm64 2.40.2-11 [47.8 kB] Fetched 47.8 kB in 0s (2738 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgoqfvfbq/uuid-dev_2.40.2-11_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 docbook all 4.5-11 [126 kB] Fetched 126 kB in 0s (7279 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppygx_veb/docbook_4.5-11_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libxss1 arm64 1:1.2.3-1+b2 [17.1 kB] Fetched 17.1 kB in 0s (1037 kB/s) dpkg-name: info: moved 'libxss1_1%3a1.2.3-1+b2_arm64.deb' to '/srv/rebuilderd/tmp/tmpgkxdfgm2/libxss1_1.2.3-1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgpg-error0 arm64 1.50-4 [78.1 kB] Fetched 78.1 kB in 0s (4505 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4jpv_gz5/libgpg-error0_1.50-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libjemalloc-dev arm64 5.3.0-2+b2 [357 kB] Fetched 357 kB in 0s (18.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzg8o0081/libjemalloc-dev_5.3.0-2+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libbz2-1.0 arm64 1.0.8-6 [37.8 kB] Fetched 37.8 kB in 0s (2184 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1te2b8ze/libbz2-1.0_1.0.8-6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmd0 arm64 1.1.0-2+b1 [33.7 kB] Fetched 33.7 kB in 0s (2015 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnkyccssm/libmd0_1.1.0-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Fetched 27.8 kB in 0s (1702 kB/s) dpkg-name: info: moved 'libxdmcp6_1%3a1.1.5-1_arm64.deb' to '/srv/rebuilderd/tmp/tmp04s5m2ts/libxdmcp6_1.1.5-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Fetched 189 kB in 0s (10.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmhqaf7t4/libelf1t64_0.192-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgio-2.0-dev-bin arm64 2.82.2-3 [162 kB] Fetched 162 kB in 0s (9185 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3bi6g266/libgio-2.0-dev-bin_2.82.2-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libice-dev arm64 2:1.1.1-1 [73.0 kB] Fetched 73.0 kB in 0s (4390 kB/s) dpkg-name: info: moved 'libice-dev_2%3a1.1.1-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpek7k58qv/libice-dev_1.1.1-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libcap-ng0 arm64 0.8.5-3+b1 [17.0 kB] Fetched 17.0 kB in 0s (1042 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6p_nybkc/libcap-ng0_0.8.5-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 protobuf-compiler arm64 3.21.12-10+b1 [84.9 kB] Fetched 84.9 kB in 0s (5031 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdxy38_ov/protobuf-compiler_3.21.12-10+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpam-runtime all 1.5.3-7 [140 kB] Fetched 140 kB in 0s (7839 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptq7ihnfl/libpam-runtime_1.5.3-7_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 tzdata all 2024b-3 [255 kB] Fetched 255 kB in 0s (13.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg1j1fya8/tzdata_2024b-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Fetched 173 kB in 0s (9554 kB/s) dpkg-name: info: moved 'libjpeg62-turbo_1%3a2.1.5-3+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmp7ao8qebc/libjpeg62-turbo_2.1.5-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libaudit1 arm64 1:4.0.2-2 [54.2 kB] Fetched 54.2 kB in 0s (3218 kB/s) dpkg-name: info: moved 'libaudit1_1%3a4.0.2-2_arm64.deb' to '/srv/rebuilderd/tmp/tmpe11mp8mk/libaudit1_4.0.2-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 sgml-data all 2.0.11+nmu1 [179 kB] Fetched 179 kB in 0s (9732 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw77ve0hg/sgml-data_2.0.11+nmu1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-9 [629 kB] Fetched 629 kB in 0s (29.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt1b4zc1d/libdb5.3t64_5.3.28+dfsg2-9_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libdebuginfod-common all 0.192-4 [23.7 kB] Fetched 23.7 kB in 0s (1367 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpshtsrc1i/libdebuginfod-common_0.192-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpcre2-posix3 arm64 10.44-4 [60.4 kB] Fetched 60.4 kB in 0s (3574 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphbc__0i7/libpcre2-posix3_10.44-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241208T204421Z sid/main arm64 cmake arm64 3.31.1-1 [9873 kB] Fetched 9873 kB in 0s (114 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjegnyc6k/cmake_3.31.1-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libunbound8 arm64 1.22.0-1 [553 kB] Fetched 553 kB in 0s (32.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq_2guszj/libunbound8_1.22.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libp11-kit0 arm64 0.25.5-2+b1 [411 kB] Fetched 411 kB in 0s (20.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbjpt1lrh/libp11-kit0_0.25.5-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 bsdutils arm64 1:2.40.2-11 [104 kB] Fetched 104 kB in 0s (5969 kB/s) dpkg-name: info: moved 'bsdutils_1%3a2.40.2-11_arm64.deb' to '/srv/rebuilderd/tmp/tmpnv575eo5/bsdutils_2.40.2-11_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 liblsan0 arm64 14.2.0-8 [1161 kB] Fetched 1161 kB in 0s (43.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpad11aszo/liblsan0_14.2.0-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 debhelper all 13.20 [915 kB] Fetched 915 kB in 0s (37.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1x652iif/debhelper_13.20_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libmount-dev arm64 2.40.2-11 [28.9 kB] Fetched 28.9 kB in 0s (1771 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqh_h9_5j/libmount-dev_2.40.2-11_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Fetched 248 kB in 0s (13.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7298xiyw/po-debconf_1.0.21+nmu1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-scales all 1.3.0-1 [677 kB] Fetched 677 kB in 0s (30.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp89nrvoxx/r-cran-scales_1.3.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libglib2.0-dev-bin arm64 2.82.2-3 [51.5 kB] Fetched 51.5 kB in 0s (3048 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf4molbm9/libglib2.0-dev-bin_2.82.2-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libstdc++-14-dev arm64 14.2.0-8 [2267 kB] Fetched 2267 kB in 0s (63.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpauvckwxt/libstdc++-14-dev_14.2.0-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Fetched 159 kB in 0s (5669 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpizhmbb3c/libreadline8t64_8.2-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 elfutils arm64 0.192-4 [464 kB] Fetched 464 kB in 0s (22.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa910l4kr/elfutils_0.192-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libraptor2-dev arm64 2.0.16-4+b1 [205 kB] Fetched 205 kB in 0s (9330 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4_07plt6/libraptor2-dev_2.0.16-4+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-cran-tibble arm64 3.2.1+dfsg-2+b1 [425 kB] Fetched 425 kB in 0s (20.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd42v5644/r-cran-tibble_3.2.1+dfsg-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 fastahack arm64 1.0.0+dfsg-11+b2 [12.2 kB] Fetched 12.2 kB in 0s (614 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgjaufona/fastahack_1.0.0+dfsg-11+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Fetched 143 kB in 0s (8086 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmwwy6hnd/libuv1t64_1.48.0-7_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 unzip arm64 6.0-28+b1 [158 kB] Fetched 158 kB in 0s (8806 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdkr0mxd3/unzip_6.0-28+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 librasqal3-dev arm64 0.9.33-2.1+b2 [224 kB] Fetched 224 kB in 0s (12.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprtvg1z4o/librasqal3-dev_0.9.33-2.1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Fetched 112 kB in 0s (6115 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaqkthibl/libnghttp2-dev_1.64.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB] Fetched 46.9 kB in 0s (2710 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptet5ywlc/libtasn1-6_4.19.0-3+b3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libsimde-dev all 0.8.2-1 [465 kB] Fetched 465 kB in 0s (23.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpivkf18dr/libsimde-dev_0.8.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libxxhash0 arm64 0.8.2-2+b2 [22.1 kB] Fetched 22.1 kB in 0s (1316 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0p4fdaiv/libxxhash0_0.8.2-2+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 xsltproc arm64 1.1.35-1.1+b1 [115 kB] Fetched 115 kB in 0s (9077 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsb35wbnj/xsltproc_1.1.35-1.1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB] Fetched 1363 kB in 0s (49.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn_v_4vd_/libgnutls30t64_3.8.8-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgcc-s1 arm64 14.2.0-8 [54.1 kB] Fetched 54.1 kB in 0s (3173 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0vf3kfj2/libgcc-s1_14.2.0-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Fetched 69.2 kB in 0s (4052 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp40xwzjtk/libuchardet0_0.0.8-1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libmount1 arm64 2.40.2-11 [190 kB] Fetched 190 kB in 0s (10.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7l95rwap/libmount1_2.40.2-11_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpng-dev arm64 1.6.44-2 [360 kB] Fetched 360 kB in 0s (18.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvo7mh4ti/libpng-dev_1.6.44-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Fetched 89.7 kB in 0s (5053 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph36cc2lo/libdebhelper-perl_13.20_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libjansson4 arm64 2.14-2+b3 [39.2 kB] Fetched 39.2 kB in 0s (2303 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7qozyogp/libjansson4_2.14-2+b3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libprotobuf32t64 arm64 3.21.12-10+b1 [859 kB] Fetched 859 kB in 0s (36.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpklliujif/libprotobuf32t64_3.21.12-10+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 build-essential arm64 12.12 [4624 B] Fetched 4624 B in 0s (431 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9edf8rnd/build-essential_12.12_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libsigsegv2 arm64 2.14-1+b2 [34.3 kB] Fetched 34.3 kB in 0s (1972 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4w9pnea3/libsigsegv2_2.14-1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libltdl7 arm64 2.4.7-8 [392 kB] Fetched 392 kB in 0s (28.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjo6h1ob9/libltdl7_2.4.7-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libelf-dev arm64 0.192-4 [94.9 kB] Fetched 94.9 kB in 0s (5628 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplpackh20/libelf-dev_0.192-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB] Fetched 446 kB in 0s (21.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppxi1_999/libgnutls-dane0t64_3.8.8-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsmithwaterman-dev arm64 0.0+git20160702.2610e25-12+b2 [37.9 kB] Fetched 37.9 kB in 0s (2234 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpajt008x3/libsmithwaterman-dev_0.0+git20160702.2610e25-12+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libmhash2 arm64 0.9.9.9-10 [94.5 kB] Fetched 94.5 kB in 0s (5437 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy1atzmez/libmhash2_0.9.9.9-10_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpam0g arm64 1.5.3-7+b1 [67.0 kB] Fetched 67.0 kB in 0s (2999 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwt25wjz7/libpam0g_1.5.3-7+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgcc-14-dev arm64 14.2.0-8 [2365 kB] Fetched 2365 kB in 0s (66.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7pdqe76q/libgcc-14-dev_14.2.0-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libhogweed6t64 arm64 3.10-1+b1 [331 kB] Fetched 331 kB in 0s (17.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjo811sis/libhogweed6t64_3.10-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 raptor2-utils arm64 2.0.16-4+b1 [34.6 kB] Fetched 34.6 kB in 0s (1838 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr9j3ua6b/raptor2-utils_2.0.16-4+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libnghttp3-9 arm64 1.4.0-1+b1 [59.6 kB] Fetched 59.6 kB in 0s (3579 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpssji073y/libnghttp3-9_1.4.0-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libsepol2 arm64 3.7-1 [264 kB] Fetched 264 kB in 0s (13.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4_na0w8j/libsepol2_3.7-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 python3.12-minimal arm64 3.12.7-3 [1940 kB] Fetched 1940 kB in 0s (60.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsb19ymvx/python3.12-minimal_3.12.7-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 readline-common all 8.2-5 [69.3 kB] Fetched 69.3 kB in 0s (3955 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwotfpirq/readline-common_8.2-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Fetched 7984 B in 0s (486 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpge41bfgo/python3-jaraco.context_6.0.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 sensible-utils all 0.0.24 [24.8 kB] Fetched 24.8 kB in 0s (1524 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp51g2sr0j/sensible-utils_0.0.24_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-magrittr arm64 2.0.3-1+b1 [203 kB] Fetched 203 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2sxs8u8k/r-cran-magrittr_2.0.3-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 bison arm64 2:3.8.2+dfsg-1+b2 [1149 kB] Fetched 1149 kB in 0s (44.6 MB/s) dpkg-name: info: moved 'bison_2%3a3.8.2+dfsg-1+b2_arm64.deb' to '/srv/rebuilderd/tmp/tmpbpm4yf7s/bison_3.8.2+dfsg-1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-cran-rlang arm64 1.1.4-1+b1 [1708 kB] Fetched 1708 kB in 0s (56.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0vyhozd6/r-cran-rlang_1.1.4-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 perl-base arm64 5.40.0-7 [1534 kB] Fetched 1534 kB in 0s (51.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpko0kourx/perl-base_5.40.0-7_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 make arm64 4.3-4.1+b1 [372 kB] Fetched 372 kB in 0s (18.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwr7_8qch/make_4.3-4.1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Fetched 115 kB in 0s (6680 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf0u_ibqz/libxcb-render0_1.17.0-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 librdf0-dev arm64 1.0.17-4+b1 [239 kB] Fetched 239 kB in 0s (13.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnka99rzi/librdf0-dev_1.0.17-4+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0-dev arm64 1.17.0-2+b1 [108 kB] Fetched 108 kB in 0s (6227 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptj8gndo3/libxcb-shm0-dev_1.17.0-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 findutils arm64 4.10.0-3 [696 kB] Fetched 696 kB in 0s (53.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjyinsqca/findutils_4.10.0-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libsysprof-capture-4-dev arm64 47.1-1 [49.1 kB] Fetched 49.1 kB in 0s (2931 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptvejx1ej/libsysprof-capture-4-dev_47.1-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Fetched 55.4 kB in 0s (3355 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm5rukza9/libsasl2-2_2.1.28+dfsg1-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 librdf0t64 arm64 1.0.17-4+b1 [100 kB] Fetched 100 kB in 0s (5559 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmv7flzmk/librdf0t64_1.0.17-4+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 dpkg arm64 1.22.11 [1514 kB] Fetched 1514 kB in 0s (51.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgcljiffu/dpkg_1.22.11_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Fetched 198 kB in 0s (10.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwzsydlo_/help2man_1.49.3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Fetched 56.8 kB in 0s (3273 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5zz7uei_/librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 x11proto-dev all 2024.1-1 [603 kB] Fetched 603 kB in 0s (27.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpid0kecsh/x11proto-dev_2024.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 gcc-14-base arm64 14.2.0-8 [47.2 kB] Fetched 47.2 kB in 0s (2838 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcq4_qwd4/gcc-14-base_14.2.0-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-cran-glue arm64 1.7.0-1+b1 [159 kB] Fetched 159 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_959ez81/r-cran-glue_1.7.0-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 rs arm64 20200313-1+b1 [15.2 kB] Fetched 15.2 kB in 0s (900 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplm6gqadn/rs_20200313-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libuuid1 arm64 2.40.2-11 [35.7 kB] Fetched 35.7 kB in 0s (2165 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8ott25ac/libuuid1_2.40.2-11_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Fetched 26.1 kB in 0s (1604 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3r4jfbya/pkgconf_1.8.1-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libglib2.0-dev arm64 2.82.2-3 [52.3 kB] Fetched 52.3 kB in 0s (3117 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5p6g93zz/libglib2.0-dev_2.82.2-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Fetched 235 kB in 0s (12.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp4n7uwsr/libssh2-1t64_1.11.1-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 openssl-provider-legacy arm64 3.3.2-2 [296 kB] Fetched 296 kB in 0s (15.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7dm1l_cf/openssl-provider-legacy_3.3.2-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 tabix arm64 1.20+ds-2 [455 kB] Fetched 455 kB in 0s (21.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprfxmf3nw/tabix_1.20+ds-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libfreetype-dev arm64 2.13.3+dfsg-1 [600 kB] Fetched 600 kB in 0s (27.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqa8q80fs/libfreetype-dev_2.13.3+dfsg-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libwfa2-dev arm64 2.3.3-4+b1 [74.9 kB] Fetched 74.9 kB in 0s (4310 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl1599t9q/libwfa2-dev_2.3.3-4+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 python3.12 arm64 3.12.7-3 [671 kB] Fetched 671 kB in 0s (31.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyw4r9g90/python3.12_3.12.7-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-munsell all 0.5.1-1 [237 kB] Fetched 237 kB in 0s (14.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpml0z0lem/r-cran-munsell_0.5.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 flex arm64 2.6.4-8.2+b3 [412 kB] Fetched 412 kB in 0s (18.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0l2h6tlz/flex_2.6.4-8.2+b3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Fetched 35.3 kB in 0s (2177 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvou9ru8g/libpkgconf3_1.8.1-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-12+b2 [32.4 kB] Fetched 32.4 kB in 0s (1935 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_mi0pjuq/libsmithwaterman0_0.0+git20160702.2610e25-12+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libmpc3 arm64 1.3.1-1+b3 [50.5 kB] Fetched 50.5 kB in 0s (3018 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf_bcrn60/libmpc3_1.3.1-1+b3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 pv arm64 1.9.0-1 [98.6 kB] Fetched 98.6 kB in 0s (5834 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx9pwig09/pv_1.9.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libglib2.0-data all 2.82.2-3 [1275 kB] Fetched 1275 kB in 0s (29.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4idj_45l/libglib2.0-data_2.82.2-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Fetched 168 kB in 0s (8759 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphuv9jlzb/libthai-data_0.1.29-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libsepol-dev arm64 3.7-1 [354 kB] Fetched 354 kB in 0s (18.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn6gomqp5/libsepol-dev_3.7-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 g++-14 arm64 14.2.0-8 [20.2 kB] Fetched 20.2 kB in 0s (1212 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9r7houbz/g++-14_14.2.0-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libselinux1-dev arm64 3.7-3+b1 [164 kB] Fetched 164 kB in 0s (9161 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0sjqs314/libselinux1-dev_3.7-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 gcc arm64 4:14.2.0-1 [5136 B] Fetched 5136 B in 0s (299 kB/s) dpkg-name: info: moved 'gcc_4%3a14.2.0-1_arm64.deb' to '/srv/rebuilderd/tmp/tmp7vzj2c69/gcc_14.2.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libdpkg-perl all 1.22.11 [644 kB] Fetched 644 kB in 0s (29.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo5fkvc6c/libdpkg-perl_1.22.11_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libcurl4t64 arm64 8.11.0-1 [322 kB] Fetched 322 kB in 0s (15.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpodow1zf5/libcurl4t64_8.11.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 dpkg-dev all 1.22.11 [1332 kB] Fetched 1332 kB in 0s (47.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1ynbm6_w/dpkg-dev_1.22.11_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Fetched 143 kB in 0s (7826 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdklwy6eo/libxcb1_1.17.0-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 python3-minimal arm64 3.12.7-1 [26.8 kB] Fetched 26.8 kB in 0s (1577 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp23wfyz9n/python3-minimal_3.12.7-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Fetched 463 kB in 0s (22.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0dpcx8m1/r-cran-pillar_1.9.0+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 liblz4-dev arm64 1.9.4-3+b1 [79.1 kB] Fetched 79.1 kB in 0s (4656 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0yqhhbe4/liblz4-dev_1.9.4-3+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Fetched 77.9 kB in 0s (4600 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc1xresiq/libpsl-dev_0.21.2-1.1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Fetched 8448 B in 0s (511 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp844gmclp/dh-strip-nondeterminism_1.14.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 gtk-doc-tools all 1.34.0-1 [328 kB] Fetched 328 kB in 0s (17.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr55002in/gtk-doc-tools_1.34.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B] Fetched 3600 B in 0s (218 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7hx692zo/libboost-program-options-dev_1.83.0.2+b2_arm64.deb' Downloading dependency 1 of 475: libidn2-0:arm64=2.3.7-2+b1 Downloading dependency 2 of 475: native-architecture:arm64=0.2.3 Downloading dependency 3 of 475: r-cran-littler:arm64=0.3.20-1+b1 Downloading dependency 4 of 475: ca-certificates:arm64=20240203 Downloading dependency 5 of 475: liblzma-dev:arm64=5.6.3-1+b1 Downloading dependency 6 of 475: libvcflib-tools:arm64=1.0.9+dfsg1-3+b2 Downloading dependency 7 of 475: libcairo-gobject2:arm64=1.18.2-2 Downloading dependency 8 of 475: libselinux1:arm64=3.7-3+b1 Downloading dependency 9 of 475: uuid-dev:arm64=2.40.2-11 Downloading dependency 10 of 475: docbook:arm64=4.5-11 Downloading dependency 11 of 475: libxss1:arm64=1:1.2.3-1+b2 Downloading dependency 12 of 475: libgpg-error0:arm64=1.50-4 Downloading dependency 13 of 475: libjemalloc-dev:arm64=5.3.0-2+b2 Downloading dependency 14 of 475: libbz2-1.0:arm64=1.0.8-6 Downloading dependency 15 of 475: libmd0:arm64=1.1.0-2+b1 Downloading dependency 16 of 475: libxdmcp6:arm64=1:1.1.5-1 Downloading dependency 17 of 475: libelf1t64:arm64=0.192-4 Downloading dependency 18 of 475: libgio-2.0-dev-bin:arm64=2.82.2-3 Downloading dependency 19 of 475: libice-dev:arm64=2:1.1.1-1 Downloading dependency 20 of 475: libcap-ng0:arm64=0.8.5-3+b1 Downloading dependency 21 of 475: protobuf-compiler:arm64=3.21.12-10+b1 Downloading dependency 22 of 475: libpam-runtime:arm64=1.5.3-7 Downloading dependency 23 of 475: tzdata:arm64=2024b-3 Downloading dependency 24 of 475: libjpeg62-turbo:arm64=1:2.1.5-3+b1 Downloading dependency 25 of 475: libaudit1:arm64=1:4.0.2-2 Downloading dependency 26 of 475: sgml-data:arm64=2.0.11+nmu1 Downloading dependency 27 of 475: libdb5.3t64:arm64=5.3.28+dfsg2-9 Downloading dependency 28 of 475: libdebuginfod-common:arm64=0.192-4 Downloading dependency 29 of 475: libpcre2-posix3:arm64=10.44-4 Downloading dependency 30 of 475: cmake:arm64=3.31.1-1 Downloading dependency 31 of 475: libunbound8:arm64=1.22.0-1 Downloading dependency 32 of 475: libp11-kit0:arm64=0.25.5-2+b1 Downloading dependency 33 of 475: bsdutils:arm64=1:2.40.2-11 Downloading dependency 34 of 475: liblsan0:arm64=14.2.0-8 Downloading dependency 35 of 475: debhelper:arm64=13.20 Downloading dependency 36 of 475: libmount-dev:arm64=2.40.2-11 Downloading dependency 37 of 475: po-debconf:arm64=1.0.21+nmu1 Downloading dependency 38 of 475: r-cran-scales:arm64=1.3.0-1 Downloading dependency 39 of 475: libglib2.0-dev-bin:arm64=2.82.2-3 Downloading dependency 40 of 475: libstdc++-14-dev:arm64=14.2.0-8 Downloading dependency 41 of 475: libreadline8t64:arm64=8.2-5 Downloading dependency 42 of 475: elfutils:arm64=0.192-4 Downloading dependency 43 of 475: libraptor2-dev:arm64=2.0.16-4+b1 Downloading dependency 44 of 475: r-cran-tibble:arm64=3.2.1+dfsg-2+b1 Downloading dependency 45 of 475: fastahack:arm64=1.0.0+dfsg-11+b2 Downloading dependency 46 of 475: libuv1t64:arm64=1.48.0-7 Downloading dependency 47 of 475: unzip:arm64=6.0-28+b1 Downloading dependency 48 of 475: librasqal3-dev:arm64=0.9.33-2.1+b2 Downloading dependency 49 of 475: libnghttp2-dev:arm64=1.64.0-1 Downloading dependency 50 of 475: libtasn1-6:arm64=4.19.0-3+b3 Downloading dependency 51 of 475: libsimde-dev:arm64=0.8.2-1 Downloading dependency 52 of 475: libxxhash0:arm64=0.8.2-2+b2 Downloading dependency 53 of 475: xsltproc:arm64=1.1.35-1.1+b1 Downloading dependency 54 of 475: libgnutls30t64:arm64=3.8.8-2 Downloading dependency 55 of 475: libgcc-s1:arm64=14.2.0-8 Downloading dependency 56 of 475: libuchardet0:arm64=0.0.8-1+b2 Downloading dependency 57 of 475: libmount1:arm64=2.40.2-11 Downloading dependency 58 of 475: libpng-dev:arm64=1.6.44-2 Downloading dependency 59 of 475: libdebhelper-perl:arm64=13.20 Downloading dependency 60 of 475: libjansson4:arm64=2.14-2+b3 Downloading dependency 61 of 475: libprotobuf32t64:arm64=3.21.12-10+b1 Downloading dependency 62 of 475: build-essential:arm64=12.12 Downloading dependency 63 of 475: libsigsegv2:arm64=2.14-1+b2 Downloading dependency 64 of 475: libltdl7:arm64=2.4.7-8 Downloading dependency 65 of 475: libelf-dev:arm64=0.192-4 Downloading dependency 66 of 475: libgnutls-dane0t64:arm64=3.8.8-2 Downloading dependency 67 of 475: libsmithwaterman-dev:arm64=0.0+git20160702.2610e25-12+b2 Downloading dependency 68 of 475: libmhash2:arm64=0.9.9.9-10 Downloading dependency 69 of 475: libpam0g:arm64=1.5.3-7+b1 Downloading dependency 70 of 475: libgcc-14-dev:arm64=14.2.0-8 Downloading dependency 71 of 475: libhogweed6t64:arm64=3.10-1+b1 Downloading dependency 72 of 475: raptor2-utils:arm64=2.0.16-4+b1 Downloading dependency 73 of 475: libnghttp3-9:arm64=1.4.0-1+b1 Downloading dependency 74 of 475: libsepol2:arm64=3.7-1 Downloading dependency 75 of 475: python3.12-minimal:arm64=3.12.7-3 Downloading dependency 76 of 475: readline-common:arm64=8.2-5 Downloading dependency 77 of 475: python3-jaraco.context:arm64=6.0.0-1 Downloading dependency 78 of 475: sensible-utils:arm64=0.0.24 Downloading dependency 79 of 475: r-cran-magrittr:arm64=2.0.3-1+b1 Downloading dependency 80 of 475: bison:arm64=2:3.8.2+dfsg-1+b2 Downloading dependency 81 of 475: r-cran-rlang:arm64=1.1.4-1+b1 Downloading dependency 82 of 475: perl-base:arm64=5.40.0-7 Downloading dependency 83 of 475: make:arm64=4.3-4.1+b1 Downloading dependency 84 of 475: libxcb-render0:arm64=1.17.0-2+b1 Downloading dependency 85 of 475: librdf0-dev:arm64=1.0.17-4+b1 Downloading dependency 86 of 475: libxcb-shm0-dev:arm64=1.17.0-2+b1 Downloading dependency 87 of 475: findutils:arm64=4.10.0-3 Downloading dependency 88 of 475: libsysprof-capture-4-dev:arm64=47.1-1 Downloading dependency 89 of 475: libsasl2-2:arm64=2.1.28+dfsg1-8 Downloading dependency 90 of 475: librdf0t64:arm64=1.0.17-4+b1 Downloading dependency 91 of 475: dpkg:arm64=1.22.11 Downloading dependency 92 of 475: help2man:arm64=1.49.3+b1 Downloading dependency 93 of 475: librtmp1:arm64=2.4+20151223.gitfa8646d.1-2+b5 Downloading dependency 94 of 475: x11proto-dev:arm64=2024.1-1 Downloading dependency 95 of 475: gcc-14-base:arm64=14.2.0-8 Downloading dependency 96 of 475: r-cran-glue:arm64=1.7.0-1+b1 Downloading dependency 97 of 475: rs:arm64=20200313-1+b1 Downloading dependency 98 of 475: libuuid1:arm64=2.40.2-11 Downloading dependency 99 of 475: pkgconf:arm64=1.8.1-4 Downloading dependency 100 of 475: libglib2.0-dev:arm64=2.82.2-3 Downloading dependency 101 of 475: libssh2-1t64:arm64=1.11.1-1 Downloading dependency 102 of 475: openssl-provider-legacy:arm64=3.3.2-2 Downloading dependency 103 of 475: tabix:arm64=1.20+ds-2 Downloading dependency 104 of 475: libfreetype-dev:arm64=2.13.3+dfsg-1 Downloading dependency 105 of 475: libwfa2-dev:arm64=2.3.3-4+b1 Downloading dependency 106 of 475: python3.12:arm64=3.12.7-3 Downloading dependency 107 of 475: r-cran-munsell:arm64=0.5.1-1 Downloading dependency 108 of 475: flex:arm64=2.6.4-8.2+b3 Downloading dependency 109 of 475: libpkgconf3:arm64=1.8.1-4 Downloading dependency 110 of 475: libsmithwaterman0:arm64=0.0+git20160702.2610e25-12+b2 Downloading dependency 111 of 475: libmpc3:arm64=1.3.1-1+b3 Downloading dependency 112 of 475: pv:arm64=1.9.0-1 Downloading dependency 113 of 475: libglib2.0-data:arm64=2.82.2-3 Downloading dependency 114 of 475: libthai-data:arm64=0.1.29-2 Downloading dependency 115 of 475: libsepol-dev:arm64=3.7-1 Downloading dependency 116 of 475: g++-14:arm64=14.2.0-8 Downloading dependency 117 of 475: libselinux1-dev:arm64=3.7-3+b1 Downloading dependency 118 of 475: gcc:arm64=4:14.2.0-1 Downloading dependency 119 of 475: libdpkg-perl:arm64=1.22.11 Downloading dependency 120 of 475: libcurl4t64:arm64=8.11.0-1 Downloading dependency 121 of 475: dpkg-dev:arm64=1.22.11 Downloading dependency 122 of 475: libxcb1:arm64=1.17.0-2+b1 Downloading dependency 123 of 475: python3-minimal:arm64=3.12.7-1 Downloading dependency 124 of 475: r-cran-pillar:arm64=1.9.0+dfsg-1 Downloading dependency 125 of 475: liblz4-dev:arm64=1.9.4-3+b1 Downloading dependency 126 of 475: libpsl-dev:arm64=0.21.2-1.1+b1 Downloading dependency 127 of 475: dh-strip-nondeterminism:arm64=1.14.0-1 Downloading dependency 128 of 475: gtk-doc-tools:arm64=1.34.0-1 Downloading dependency 129 of 475: libboost-program-options-dev:arm64=1.83.0.2+b2 Downloading dependency 130 of 475: python3-more-itertools:arm64=10.5.0-1Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Fetched 63.8 kB in 0s (3780 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprn8tbktv/python3-more-itertools_10.5.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 autotools-dev all 20220109.1 [51.6 kB] Fetched 51.6 kB in 0s (3122 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvwzhli3i/autotools-dev_20220109.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libldap-dev arm64 2.5.18+dfsg-3+b1 [300 kB] Fetched 300 kB in 0s (15.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_q33mpyx/libldap-dev_2.5.18+dfsg-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-cran-rcpp arm64 1.0.13-1-1 [2057 kB] Fetched 2057 kB in 0s (61.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn2y_u5rl/r-cran-rcpp_1.0.13-1-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 bc arm64 1.07.1-4+b1 [101 kB] Fetched 101 kB in 0s (5670 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7lstcvzp/bc_1.07.1-4+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Fetched 75.5 kB in 0s (4489 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp82ehgmar/xdg-utils_1.1.3-4.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Fetched 314 kB in 0s (16.3 MB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.45-3+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmpifojf2rv/libmagic-mgc_5.45-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpango-1.0-0 arm64 1.54.0+ds-3 [210 kB] Fetched 210 kB in 0s (11.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm5lujfma/libpango-1.0-0_1.54.0+ds-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 python3 arm64 3.12.7-1 [27.8 kB] Fetched 27.8 kB in 0s (1669 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbky_2hfx/python3_3.12.7-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Fetched 836 kB in 0s (35.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0mdeu9p8/python3-pygments_2.18.0+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libngtcp2-dev arm64 1.6.0-1 [165 kB] Fetched 165 kB in 0s (7749 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj8mh_njz/libngtcp2-dev_1.6.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-cran-r6 all 2.5.1-1 [105 kB] Fetched 105 kB in 0s (5844 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3u76npiw/r-cran-r6_2.5.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 usr-is-merged all 39 [5572 B] Fetched 5572 B in 0s (343 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf__2wdtq/usr-is-merged_39_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Fetched 78.7 kB in 0s (4667 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp066_g1z0/libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Fetched 361 kB in 0s (18.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk2q6_a5j/libgfortran5_14.2.0-8_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Fetched 228 kB in 0s (12.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuvx1knvg/r-cran-gtable_0.3.6+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 zlib1g arm64 1:1.3.dfsg+really1.3.1-1+b1 [85.1 kB] Fetched 85.1 kB in 0s (4983 kB/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmptosd6uqd/zlib1g_1.3.dfsg+really1.3.1-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Fetched 630 kB in 0s (29.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpct88g8hm/libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 hostname arm64 3.25 [10.8 kB] Fetched 10.8 kB in 0s (664 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphncry16m/hostname_3.25_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-cran-lattice arm64 0.22-6-1+b1 [1417 kB] Fetched 1417 kB in 0s (50.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptf_ffsl9/r-cran-lattice_0.22-6-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libnghttp3-dev arm64 1.4.0-1+b1 [85.2 kB] Fetched 85.2 kB in 0s (4789 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpus3ss7m7/libnghttp3-dev_1.4.0-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Fetched 13.6 kB in 0s (720 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy5_1tt_g/python3-autocommand_2.2.2-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libtk8.6 arm64 8.6.15-1 [738 kB] Fetched 738 kB in 0s (32.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn0b1lk1s/libtk8.6_8.6.15-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-cran-matrix arm64 1.7-1-1 [4023 kB] Fetched 4023 kB in 0s (82.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjqx654ye/r-cran-matrix_1.7-1-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgdbm-compat4t64 arm64 1.24-2 [50.3 kB] Fetched 50.3 kB in 0s (3016 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjcjam0y4/libgdbm-compat4t64_1.24-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libprotobuf-dev arm64 3.21.12-10+b1 [1261 kB] Fetched 1261 kB in 0s (46.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbdg3nsvk/libprotobuf-dev_3.21.12-10+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libncursesw6 arm64 6.5-2+b1 [125 kB] Fetched 125 kB in 0s (8135 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqz88jxw2/libncursesw6_6.5-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 cpp-14 arm64 14.2.0-8 [1284 B] Fetched 1284 B in 0s (78.1 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1bdlrpy4/cpp-14_14.2.0-8_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Fetched 62.1 kB in 0s (3541 kB/s) dpkg-name: info: moved 'libice6_2%3a1.1.1-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpl9n4whp_/libice6_1.1.1-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libdivsufsort-dev arm64 2.0.1-6+b1 [19.1 kB] Fetched 19.1 kB in 0s (1155 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqjw78irw/libdivsufsort-dev_2.0.1-6+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libxext-dev arm64 2:1.3.4-1+b2 [105 kB] Fetched 105 kB in 0s (5815 kB/s) dpkg-name: info: moved 'libxext-dev_2%3a1.3.4-1+b2_arm64.deb' to '/srv/rebuilderd/tmp/tmp0ktz6tzo/libxext-dev_1.3.4-1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpam-modules arm64 1.5.3-7+b1 [261 kB] Fetched 261 kB in 0s (13.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptfy8qsf0/libpam-modules_1.5.3-7+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libcrypt1 arm64 1:4.4.36-5 [91.6 kB] Fetched 91.6 kB in 0s (5440 kB/s) dpkg-name: info: moved 'libcrypt1_1%3a4.4.36-5_arm64.deb' to '/srv/rebuilderd/tmp/tmpue675z0t/libcrypt1_4.4.36-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgmp10 arm64 2:6.3.0+dfsg-2+b2 [535 kB] Fetched 535 kB in 0s (26.0 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-2+b2_arm64.deb' to '/srv/rebuilderd/tmp/tmpqiixc3o0/libgmp10_6.3.0+dfsg-2+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 python3-lxml arm64 5.3.0-1+b1 [1433 kB] Fetched 1433 kB in 0s (49.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx8e6b1m1/python3-lxml_5.3.0-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libxft2 arm64 2.3.6-1+b2 [51.6 kB] Fetched 51.6 kB in 0s (3097 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0f6z741h/libxft2_2.3.6-1+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 rpcsvc-proto arm64 1.4.3-1+b1 [60.5 kB] Fetched 60.5 kB in 0s (3436 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqkk7tam5/rpcsvc-proto_1.4.3-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Fetched 29.1 kB in 0s (1728 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1ep2tpsz/r-cran-pkgkitten_0.2.4-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-plyr arm64 1.8.9-1+b1 [791 kB] Fetched 791 kB in 0s (34.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd82ahu19/r-cran-plyr_1.8.9-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libitm1 arm64 14.2.0-8 [24.2 kB] Fetched 24.2 kB in 0s (1389 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2p94ehil/libitm1_14.2.0-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-cran-cli arm64 3.6.3-1 [1340 kB] Fetched 1340 kB in 0s (86.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmacmkxu1/r-cran-cli_3.6.3-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Fetched 273 kB in 0s (14.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4dxlfzks/libpng16-16t64_1.6.44-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Fetched 98.7 kB in 0s (5693 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbc90nb5z/libblas3_3.12.0-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libc-dev-bin arm64 2.40-3 [50.9 kB] Fetched 50.9 kB in 0s (3104 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo0yzv6f2/libc-dev-bin_2.40-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Fetched 198 kB in 0s (11.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuhuel5lj/gettext-base_0.22.5-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 perl-modules-5.40 all 5.40.0-7 [3017 kB] Fetched 3017 kB in 0s (74.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp232e91qy/perl-modules-5.40_5.40.0-7_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpcre2-16-0 arm64 10.44-4 [230 kB] Fetched 230 kB in 0s (12.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo8cbu1y9/libpcre2-16-0_10.44-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libdivsufsort3 arm64 2.0.1-6+b1 [39.9 kB] Fetched 39.9 kB in 0s (2233 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgpjny8tx/libdivsufsort3_2.0.1-6+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Fetched 309 kB in 0s (16.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd2g5m3wg/libtiff6_4.5.1+git230720-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8 [9166 kB] Fetched 9166 kB in 0s (111 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3rvvgt0x/cpp-14-aarch64-linux-gnu_14.2.0-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libcairo-script-interpreter2 arm64 1.18.2-2 [57.4 kB] Fetched 57.4 kB in 0s (3411 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplcoe5voy/libcairo-script-interpreter2_1.18.2-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 gcc-14 arm64 14.2.0-8 [519 kB] Fetched 519 kB in 0s (24.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpau9yz2y_/gcc-14_14.2.0-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Fetched 308 kB in 0s (15.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd4vl8j0_/libbrotli-dev_1.1.0-2+b6_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgio-2.0-dev arm64 2.82.2-3 [1691 kB] Fetched 1691 kB in 0s (55.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2vlaxfgw/libgio-2.0-dev_2.82.2-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libcairo2-dev arm64 1.18.2-2 [43.0 kB] Fetched 43.0 kB in 0s (3995 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpedwkxyo1/libcairo2-dev_1.18.2-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libprotoc32t64 arm64 3.21.12-10+b1 [789 kB] Fetched 789 kB in 0s (34.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppdwbpe0y/libprotoc32t64_3.21.12-10+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Fetched 18.5 kB in 0s (1111 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5tf10b_d/libngtcp2-crypto-gnutls8_1.6.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Fetched 441 kB in 0s (21.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgoc84tfm/libharfbuzz0b_10.0.1-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Fetched 420 kB in 0s (20.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5b0rvbfj/libhts3t64_1.20+ds-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 binutils arm64 2.43.1-5 [67.8 kB] Fetched 67.8 kB in 0s (3970 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9p8p5hm8/binutils_2.43.1-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libdw-dev arm64 0.192-4 [320 kB] Fetched 320 kB in 0s (16.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6v690_bf/libdw-dev_0.192-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-cran-mass arm64 7.3-61-1+b1 [1112 kB] Fetched 1112 kB in 0s (41.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9378arr3/r-cran-mass_7.3-61-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241208T204421Z sid/main arm64 cmake-data all 3.31.1-1 [2267 kB] Fetched 2267 kB in 0s (64.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6_exf4gr/cmake-data_3.31.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpaper1 arm64 1.1.29+b2 [13.0 kB] Fetched 13.0 kB in 0s (777 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2r6kdtcs/libpaper1_1.1.29+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Fetched 37.0 kB in 0s (2207 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkwallq30/python3-typeguard_4.4.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 automake all 1:1.16.5-1.3 [823 kB] Fetched 823 kB in 0s (35.6 MB/s) dpkg-name: info: moved 'automake_1%3a1.16.5-1.3_all.deb' to '/srv/rebuilderd/tmp/tmpnulik451/automake_1.16.5-1.3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Fetched 175 kB in 0s (9730 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpye6b0kid/libldap-2.5-0_2.5.18+dfsg-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libsmartcols1 arm64 2.40.2-11 [135 kB] Fetched 135 kB in 0s (7811 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1g8qaf8r/libsmartcols1_2.40.2-11_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Fetched 43.4 kB in 0s (2675 kB/s) dpkg-name: info: moved 'file_1%3a5.45-3+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmptwobi3bk/file_5.45-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-2+b2 [329 kB] Fetched 329 kB in 0s (16.9 MB/s) dpkg-name: info: moved 'libgmpxx4ldbl_2%3a6.3.0+dfsg-2+b2_arm64.deb' to '/srv/rebuilderd/tmp/tmp6cyczhsa/libgmpxx4ldbl_6.3.0+dfsg-2+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libboost1.83-dev arm64 1.83.0-3.2+b1 [10.6 MB] Fetched 10.6 MB in 0s (118 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt114ds7a/libboost1.83-dev_1.83.0-3.2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Fetched 48.4 kB in 0s (2801 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp36x_a34i/libthai0_0.1.29-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Fetched 23.1 kB in 0s (1413 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsokswivl/libcom-err2_1.47.1-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Fetched 96.5 kB in 0s (2813 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm38w1at0/libtasn1-6-dev_4.19.0-3+b3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 gzip arm64 1.12-1.1+b1 [131 kB] Fetched 131 kB in 0s (7317 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd2xp9zi1/gzip_1.12-1.1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpcre2-32-0 arm64 10.44-4 [220 kB] Fetched 220 kB in 0s (11.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8vggciwq/libpcre2-32-0_10.44-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 python3-packaging all 24.2-1 [55.3 kB] Fetched 55.3 kB in 0s (3340 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvupihubk/python3-packaging_24.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 xtrans-dev all 1.4.0-1 [98.7 kB] Fetched 98.7 kB in 0s (5656 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn3i60b8c/xtrans-dev_1.4.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Fetched 112 kB in 0s (6255 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9dhyyzq7/libngtcp2-16_1.6.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Fetched 57.1 kB in 0s (3295 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmply29kybf/libpsl5t64_0.21.2-1.1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libncurses-dev arm64 6.5-2+b1 [338 kB] Fetched 338 kB in 0s (17.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph09oqtb5/libncurses-dev_6.5-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpython3.12-minimal arm64 3.12.7-3 [808 kB] Fetched 808 kB in 0s (34.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb318vcxu/libpython3.12-minimal_3.12.7-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libyajl2 arm64 2.1.0-5+b2 [22.5 kB] Fetched 22.5 kB in 0s (1315 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnfkjunvl/libyajl2_2.1.0-5+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 diffutils arm64 1:3.10-1+b1 [373 kB] Fetched 373 kB in 0s (18.4 MB/s) dpkg-name: info: moved 'diffutils_1%3a3.10-1+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmp111aakcx/diffutils_3.10-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libdebconfclient0 arm64 0.273 [10.3 kB] Fetched 10.3 kB in 0s (955 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3kco2ilj/libdebconfclient0_0.273_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 debianutils arm64 5.21 [92.1 kB] Fetched 92.1 kB in 0s (5403 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl3dy98hw/debianutils_5.21_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libicu-dev arm64 72.1-5+b1 [10.3 MB] Fetched 10.3 MB in 0s (116 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoa_8rlc2/libicu-dev_72.1-5+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libasan8 arm64 14.2.0-8 [2579 kB] Fetched 2579 kB in 0s (68.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1n576h30/libasan8_14.2.0-8_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtabixpp-dev arm64 1.1.2-2.1+b1 [9052 B] Fetched 9052 B in 0s (538 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc5en7sg_/libtabixpp-dev_1.1.2-2.1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 xxd arm64 2:9.1.0861-1 [97.7 kB] Fetched 97.7 kB in 0s (5744 kB/s) dpkg-name: info: moved 'xxd_2%3a9.1.0861-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpoei1r1s8/xxd_9.1.0861-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Fetched 37.9 kB in 0s (2244 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb0l5ncoc/libnsl2_1.3.0-3+b3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Fetched 489 kB in 0s (23.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnmj_ds6f/fonts-dejavu-mono_2.37-8_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 m4 arm64 1.4.19-4 [277 kB] Fetched 277 kB in 0s (14.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp97_t44hr/m4_1.4.19-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libprotobuf-lite32t64 arm64 3.21.12-10+b1 [250 kB] Fetched 250 kB in 0s (13.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwe45enom/libprotobuf-lite32t64_3.21.12-10+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 dh-autoreconf all 20 [17.1 kB] Fetched 17.1 kB in 0s (1061 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpttqtb14k/dh-autoreconf_20_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB] Fetched 1404 kB in 0s (53.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp613kcz2b/libgnutls28-dev_3.8.8-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.6.0-1 [23.7 kB] Fetched 23.7 kB in 0s (1415 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph23dzzmh/libngtcp2-crypto-gnutls-dev_1.6.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 opensp arm64 1.5.2-15+b1 [444 kB] Fetched 444 kB in 0s (22.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpub3_dk4f/opensp_1.5.2-15+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Fetched 129 kB in 0s (7395 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0fhyvsi5/librhash1_1.4.5-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 binutils-aarch64-linux-gnu arm64 2.43.1-5 [2800 kB] Fetched 2800 kB in 0s (71.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqyh_pe42/binutils-aarch64-linux-gnu_2.43.1-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 docbook-xsl all 1.79.2+dfsg-7 [1221 kB] Fetched 1221 kB in 0s (45.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpktb_dmel/docbook-xsl_1.79.2+dfsg-7_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-cran-vctrs arm64 0.6.5-1+b1 [1378 kB] Fetched 1378 kB in 0s (47.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr1atfg8_/r-cran-vctrs_0.6.5-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 dash arm64 0.5.12-9+b1 [91.4 kB] Fetched 91.4 kB in 0s (5397 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkf9_z8nd/dash_0.5.12-9+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Fetched 72.9 kB in 0s (4343 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6mreg86m/libjsoncpp26_1.9.6-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxau-dev arm64 1:1.0.11-1 [23.9 kB] Fetched 23.9 kB in 0s (1465 kB/s) dpkg-name: info: moved 'libxau-dev_1%3a1.0.11-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpjn2l89yv/libxau-dev_1.0.11-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Fetched 22.1 kB in 0s (1366 kB/s) dpkg-name: info: moved 'xorg-sgml-doctools_1%3a1.11-1.1_all.deb' to '/srv/rebuilderd/tmp/tmpafsyb__c/xorg-sgml-doctools_1.11-1.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libfontconfig-dev arm64 2.15.0-1.1+b1 [411 kB] Fetched 411 kB in 0s (20.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplsy710oc/libfontconfig-dev_2.15.0-1.1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Fetched 31.9 kB in 0s (1964 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0ygnia2m/libbz2-dev_1.0.8-6_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libperl5.40 arm64 5.40.0-7 [4156 kB] Fetched 4156 kB in 0s (83.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu4uxxyuz/libperl5.40_5.40.0-7_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB] Fetched 1626 kB in 0s (52.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcfrft43x/libhts-dev_1.20+ds-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-4+b2 [4920 B] Fetched 4920 B in 0s (301 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0ekl8gox/libdisorder0_0.0.2+git20130809.8062ee1-4+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Fetched 789 kB in 0s (35.0 MB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.10-2_arm64.deb' to '/srv/rebuilderd/tmp/tmp77reool7/libx11-6_1.8.10-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libc-bin arm64 2.40-3 [540 kB] Fetched 540 kB in 0s (26.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp034w9mlp/libc-bin_2.40-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 cpp arm64 4:14.2.0-1 [1568 B] Fetched 1568 B in 0s (96.3 kB/s) dpkg-name: info: moved 'cpp_4%3a14.2.0-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpnac3ef5z/cpp_14.2.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Fetched 91.2 kB in 0s (5338 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqsuswe4r/bsdextrautils_2.40.2-11_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 liblzma5 arm64 5.6.3-1+b1 [266 kB] Fetched 266 kB in 0s (14.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpttccb4_3/liblzma5_5.6.3-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libx11-dev arm64 2:1.8.10-2 [877 kB] Fetched 877 kB in 0s (37.7 MB/s) dpkg-name: info: moved 'libx11-dev_2%3a1.8.10-2_arm64.deb' to '/srv/rebuilderd/tmp/tmp2fewk0ok/libx11-dev_1.8.10-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Fetched 12.0 kB in 0s (720 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplesfb_x8/python3-jaraco.functools_4.1.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 netbase all 6.4 [12.8 kB] Fetched 12.8 kB in 0s (763 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe2zbj_se/netbase_6.4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libcap2 arm64 1:2.66-5+b1 [27.2 kB] Fetched 27.2 kB in 0s (1667 kB/s) dpkg-name: info: moved 'libcap2_1%3a2.66-5+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmpgt8y0f8g/libcap2_2.66-5+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libctf-nobfd0 arm64 2.43.1-5 [151 kB] Fetched 151 kB in 0s (8617 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpntez3bfu/libctf-nobfd0_2.43.1-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libosp5 arm64 1.5.2-15+b1 [925 kB] Fetched 925 kB in 0s (39.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2yq7_hvu/libosp5_1.5.2-15+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libseccomp2 arm64 2.5.5-1+b3 [46.8 kB] Fetched 46.8 kB in 0s (2821 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfifbtjfw/libseccomp2_2.5.5-1+b3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-viridislite all 0.4.2-2 [1299 kB] Fetched 1299 kB in 0s (48.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxdlmjomx/r-cran-viridislite_0.4.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libzstd1 arm64 1.5.6+dfsg-1+b1 [261 kB] Fetched 261 kB in 0s (13.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpejfq30h7/libzstd1_1.5.6+dfsg-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libunistring5 arm64 1.2-1+b1 [417 kB] Fetched 417 kB in 0s (21.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjg78bnjj/libunistring5_1.2-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Fetched 318 kB in 0s (22.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq_51b5uf/fontconfig-config_2.15.0-1.1+b1_arm64.deb' Downloading dependency 131 of 475: autotools-dev:arm64=20220109.1 Downloading dependency 132 of 475: libldap-dev:arm64=2.5.18+dfsg-3+b1 Downloading dependency 133 of 475: r-cran-rcpp:arm64=1.0.13-1-1 Downloading dependency 134 of 475: bc:arm64=1.07.1-4+b1 Downloading dependency 135 of 475: xdg-utils:arm64=1.1.3-4.1 Downloading dependency 136 of 475: libmagic-mgc:arm64=1:5.45-3+b1 Downloading dependency 137 of 475: libpango-1.0-0:arm64=1.54.0+ds-3 Downloading dependency 138 of 475: python3:arm64=3.12.7-1 Downloading dependency 139 of 475: python3-pygments:arm64=2.18.0+dfsg-1 Downloading dependency 140 of 475: libngtcp2-dev:arm64=1.6.0-1 Downloading dependency 141 of 475: r-cran-r6:arm64=2.5.1-1 Downloading dependency 142 of 475: usr-is-merged:arm64=39 Downloading dependency 143 of 475: libtirpc3t64:arm64=1.3.4+ds-1.3+b1 Downloading dependency 144 of 475: libgfortran5:arm64=14.2.0-8 Downloading dependency 145 of 475: r-cran-gtable:arm64=0.3.6+dfsg-1 Downloading dependency 146 of 475: zlib1g:arm64=1:1.3.dfsg+really1.3.1-1+b1 Downloading dependency 147 of 475: libxml2:arm64=2.12.7+dfsg+really2.9.14-0.2+b1 Downloading dependency 148 of 475: hostname:arm64=3.25 Downloading dependency 149 of 475: r-cran-lattice:arm64=0.22-6-1+b1 Downloading dependency 150 of 475: libnghttp3-dev:arm64=1.4.0-1+b1 Downloading dependency 151 of 475: python3-autocommand:arm64=2.2.2-3 Downloading dependency 152 of 475: libtk8.6:arm64=8.6.15-1 Downloading dependency 153 of 475: r-cran-matrix:arm64=1.7-1-1 Downloading dependency 154 of 475: libgdbm-compat4t64:arm64=1.24-2 Downloading dependency 155 of 475: libprotobuf-dev:arm64=3.21.12-10+b1 Downloading dependency 156 of 475: libncursesw6:arm64=6.5-2+b1 Downloading dependency 157 of 475: cpp-14:arm64=14.2.0-8 Downloading dependency 158 of 475: libice6:arm64=2:1.1.1-1 Downloading dependency 159 of 475: libdivsufsort-dev:arm64=2.0.1-6+b1 Downloading dependency 160 of 475: libxext-dev:arm64=2:1.3.4-1+b2 Downloading dependency 161 of 475: libpam-modules:arm64=1.5.3-7+b1 Downloading dependency 162 of 475: libcrypt1:arm64=1:4.4.36-5 Downloading dependency 163 of 475: libgmp10:arm64=2:6.3.0+dfsg-2+b2 Downloading dependency 164 of 475: python3-lxml:arm64=5.3.0-1+b1 Downloading dependency 165 of 475: libxft2:arm64=2.3.6-1+b2 Downloading dependency 166 of 475: rpcsvc-proto:arm64=1.4.3-1+b1 Downloading dependency 167 of 475: r-cran-pkgkitten:arm64=0.2.4-1 Downloading dependency 168 of 475: r-cran-plyr:arm64=1.8.9-1+b1 Downloading dependency 169 of 475: libitm1:arm64=14.2.0-8 Downloading dependency 170 of 475: r-cran-cli:arm64=3.6.3-1 Downloading dependency 171 of 475: libpng16-16t64:arm64=1.6.44-2 Downloading dependency 172 of 475: libblas3:arm64=3.12.0-4 Downloading dependency 173 of 475: libc-dev-bin:arm64=2.40-3 Downloading dependency 174 of 475: gettext-base:arm64=0.22.5-2 Downloading dependency 175 of 475: perl-modules-5.40:arm64=5.40.0-7 Downloading dependency 176 of 475: libpcre2-16-0:arm64=10.44-4 Downloading dependency 177 of 475: libdivsufsort3:arm64=2.0.1-6+b1 Downloading dependency 178 of 475: libtiff6:arm64=4.5.1+git230720-5 Downloading dependency 179 of 475: cpp-14-aarch64-linux-gnu:arm64=14.2.0-8 Downloading dependency 180 of 475: libcairo-script-interpreter2:arm64=1.18.2-2 Downloading dependency 181 of 475: gcc-14:arm64=14.2.0-8 Downloading dependency 182 of 475: libbrotli-dev:arm64=1.1.0-2+b6 Downloading dependency 183 of 475: libgio-2.0-dev:arm64=2.82.2-3 Downloading dependency 184 of 475: libcairo2-dev:arm64=1.18.2-2 Downloading dependency 185 of 475: libprotoc32t64:arm64=3.21.12-10+b1 Downloading dependency 186 of 475: libngtcp2-crypto-gnutls8:arm64=1.6.0-1 Downloading dependency 187 of 475: libharfbuzz0b:arm64=10.0.1-1 Downloading dependency 188 of 475: libhts3t64:arm64=1.20+ds-2 Downloading dependency 189 of 475: binutils:arm64=2.43.1-5 Downloading dependency 190 of 475: libdw-dev:arm64=0.192-4 Downloading dependency 191 of 475: r-cran-mass:arm64=7.3-61-1+b1 Downloading dependency 192 of 475: cmake-data:arm64=3.31.1-1 Downloading dependency 193 of 475: libpaper1:arm64=1.1.29+b2 Downloading dependency 194 of 475: python3-typeguard:arm64=4.4.1-1 Downloading dependency 195 of 475: automake:arm64=1:1.16.5-1.3 Downloading dependency 196 of 475: libldap-2.5-0:arm64=2.5.18+dfsg-3+b1 Downloading dependency 197 of 475: libsmartcols1:arm64=2.40.2-11 Downloading dependency 198 of 475: file:arm64=1:5.45-3+b1 Downloading dependency 199 of 475: libgmpxx4ldbl:arm64=2:6.3.0+dfsg-2+b2 Downloading dependency 200 of 475: libboost1.83-dev:arm64=1.83.0-3.2+b1 Downloading dependency 201 of 475: libthai0:arm64=0.1.29-2+b1 Downloading dependency 202 of 475: libcom-err2:arm64=1.47.1-1+b1 Downloading dependency 203 of 475: libtasn1-6-dev:arm64=4.19.0-3+b3 Downloading dependency 204 of 475: gzip:arm64=1.12-1.1+b1 Downloading dependency 205 of 475: libpcre2-32-0:arm64=10.44-4 Downloading dependency 206 of 475: python3-packaging:arm64=24.2-1 Downloading dependency 207 of 475: xtrans-dev:arm64=1.4.0-1 Downloading dependency 208 of 475: libngtcp2-16:arm64=1.6.0-1 Downloading dependency 209 of 475: libpsl5t64:arm64=0.21.2-1.1+b1 Downloading dependency 210 of 475: libncurses-dev:arm64=6.5-2+b1 Downloading dependency 211 of 475: libpython3.12-minimal:arm64=3.12.7-3 Downloading dependency 212 of 475: libyajl2:arm64=2.1.0-5+b2 Downloading dependency 213 of 475: diffutils:arm64=1:3.10-1+b1 Downloading dependency 214 of 475: libdebconfclient0:arm64=0.273 Downloading dependency 215 of 475: debianutils:arm64=5.21 Downloading dependency 216 of 475: libicu-dev:arm64=72.1-5+b1 Downloading dependency 217 of 475: libasan8:arm64=14.2.0-8 Downloading dependency 218 of 475: libtabixpp-dev:arm64=1.1.2-2.1+b1 Downloading dependency 219 of 475: xxd:arm64=2:9.1.0861-1 Downloading dependency 220 of 475: libnsl2:arm64=1.3.0-3+b3 Downloading dependency 221 of 475: fonts-dejavu-mono:arm64=2.37-8 Downloading dependency 222 of 475: m4:arm64=1.4.19-4 Downloading dependency 223 of 475: libprotobuf-lite32t64:arm64=3.21.12-10+b1 Downloading dependency 224 of 475: dh-autoreconf:arm64=20 Downloading dependency 225 of 475: libgnutls28-dev:arm64=3.8.8-2 Downloading dependency 226 of 475: libngtcp2-crypto-gnutls-dev:arm64=1.6.0-1 Downloading dependency 227 of 475: opensp:arm64=1.5.2-15+b1 Downloading dependency 228 of 475: librhash1:arm64=1.4.5-1 Downloading dependency 229 of 475: binutils-aarch64-linux-gnu:arm64=2.43.1-5 Downloading dependency 230 of 475: docbook-xsl:arm64=1.79.2+dfsg-7 Downloading dependency 231 of 475: r-cran-vctrs:arm64=0.6.5-1+b1 Downloading dependency 232 of 475: dash:arm64=0.5.12-9+b1 Downloading dependency 233 of 475: libjsoncpp26:arm64=1.9.6-3 Downloading dependency 234 of 475: libxau-dev:arm64=1:1.0.11-1 Downloading dependency 235 of 475: xorg-sgml-doctools:arm64=1:1.11-1.1 Downloading dependency 236 of 475: libfontconfig-dev:arm64=2.15.0-1.1+b1 Downloading dependency 237 of 475: libbz2-dev:arm64=1.0.8-6 Downloading dependency 238 of 475: libperl5.40:arm64=5.40.0-7 Downloading dependency 239 of 475: libhts-dev:arm64=1.20+ds-2 Downloading dependency 240 of 475: libdisorder0:arm64=0.0.2+git20130809.8062ee1-4+b2 Downloading dependency 241 of 475: libx11-6:arm64=2:1.8.10-2 Downloading dependency 242 of 475: libc-bin:arm64=2.40-3 Downloading dependency 243 of 475: cpp:arm64=4:14.2.0-1 Downloading dependency 244 of 475: bsdextrautils:arm64=2.40.2-11 Downloading dependency 245 of 475: liblzma5:arm64=5.6.3-1+b1 Downloading dependency 246 of 475: libx11-dev:arm64=2:1.8.10-2 Downloading dependency 247 of 475: python3-jaraco.functools:arm64=4.1.0-1 Downloading dependency 248 of 475: netbase:arm64=6.4 Downloading dependency 249 of 475: libcap2:arm64=1:2.66-5+b1 Downloading dependency 250 of 475: libctf-nobfd0:arm64=2.43.1-5 Downloading dependency 251 of 475: libosp5:arm64=1.5.2-15+b1 Downloading dependency 252 of 475: libseccomp2:arm64=2.5.5-1+b3 Downloading dependency 253 of 475: r-cran-viridislite:arm64=0.4.2-2 Downloading dependency 254 of 475: libzstd1:arm64=1.5.6+dfsg-1+b1 Downloading dependency 255 of 475: libunistring5:arm64=1.2-1+b1 Downloading dependency 256 of 475: fontconfig-config:arm64=2.15.0-1.1+b1 Downloading dependency 257 of 475: patch:arm64=2.7.6-7+b1Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 patch arm64 2.7.6-7+b1 [118 kB] Fetched 118 kB in 0s (6544 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq17e_gh2/patch_2.7.6-7+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 samtools arm64 1.20-3+b1 [629 kB] Fetched 629 kB in 0s (28.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwg69hlt9/samtools_1.20-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b1 [173 kB] Fetched 173 kB in 0s (9585 kB/s) dpkg-name: info: moved 'libxt6t64_1%3a1.2.1-1.2+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmp34ci37k2/libxt6t64_1.2.1-1.2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libbackward-cpp-dev all 1.6-1 [34.3 kB] Fetched 34.3 kB in 0s (2067 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpna_aofse/libbackward-cpp-dev_1.6-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB] Fetched 122 kB in 0s (7068 kB/s) dpkg-name: info: moved 'libcrypt-dev_1%3a4.4.36-5_arm64.deb' to '/srv/rebuilderd/tmp/tmp0qr4j33v/libcrypt-dev_4.4.36-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 xz-utils arm64 5.6.3-1+b1 [540 kB] Fetched 540 kB in 0s (26.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0oece5w9/xz-utils_5.6.3-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-gridbase all 0.4-7-5 [163 kB] Fetched 163 kB in 0s (12.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8mssevij/r-cran-gridbase_0.4-7-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Fetched 19.6 kB in 0s (1193 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpndf33795/r-cran-pkgconfig_2.0.3-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libxslt1.1 arm64 1.1.35-1.1+b1 [222 kB] Fetched 222 kB in 0s (12.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1rbj_e4_/libxslt1.1_1.1.35-1.1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 autoconf all 2.72-3 [493 kB] Fetched 493 kB in 0s (23.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeqbra486/autoconf_2.72-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Fetched 168 kB in 0s (9280 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxcg_zd0y/libpixman-1-0_0.44.0-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 sed arm64 4.9-2+b1 [326 kB] Fetched 326 kB in 0s (17.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmm1i91qd/sed_4.9-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libdisorder-dev arm64 0.0.2+git20130809.8062ee1-4+b2 [4888 B] Fetched 4888 B in 0s (300 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmwyv3pct/libdisorder-dev_0.0.2+git20130809.8062ee1-4+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Fetched 20.9 kB in 0s (1294 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwrgins5t/libffi8_3.4.6-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libkdb5-10t64 arm64 1.21.3-3 [40.8 kB] Fetched 40.8 kB in 0s (2548 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdhqjxvwd/libkdb5-10t64_1.21.3-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Fetched 74.6 kB in 0s (4482 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8_0bj6n3/libhtscodecs2_1.6.1-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libnettle8t64 arm64 3.10-1+b1 [309 kB] Fetched 309 kB in 0s (16.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq0rmcjbs/libnettle8t64_3.10-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 util-linux arm64 2.40.2-11 [1170 kB] Fetched 1170 kB in 0s (45.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplpuklv41/util-linux_2.40.2-11_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 autopoint all 0.22.5-2 [723 kB] Fetched 723 kB in 0s (32.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr8a4gmz5/autopoint_0.22.5-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Fetched 310 kB in 0s (16.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbwsnzl10/libkrb5-3_1.21.3-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Fetched 34.2 kB in 0s (2083 kB/s) dpkg-name: info: moved 'libsm6_2%3a1.2.4-1_arm64.deb' to '/srv/rebuilderd/tmp/tmp2c6ysc7_/libsm6_1.2.4-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libhwasan0 arm64 14.2.0-8 [1442 kB] Fetched 1442 kB in 0s (49.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp331_bp3k/libhwasan0_14.2.0-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 x11-common all 1:7.7+23.1 [216 kB] Fetched 216 kB in 0s (11.8 MB/s) dpkg-name: info: moved 'x11-common_1%3a7.7+23.1_all.deb' to '/srv/rebuilderd/tmp/tmpf1s1x8zy/x11-common_7.7+23.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Fetched 840 kB in 0s (36.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpud7ftmvb/fonts-dejavu-core_2.37-8_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libboost-program-options1.83.0 arm64 1.83.0-3.2+b1 [331 kB] Fetched 331 kB in 0s (18.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbxj062vd/libboost-program-options1.83.0_1.83.0-3.2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-utf8 arm64 1.2.4-1+b1 [133 kB] Fetched 133 kB in 0s (7625 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcx_3wav2/r-cran-utf8_1.2.4-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libwfa2-0 arm64 2.3.3-4+b1 [55.2 kB] Fetched 55.2 kB in 0s (3339 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdra06tvy/libwfa2-0_2.3.3-4+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Fetched 20.6 kB in 0s (1267 kB/s) dpkg-name: info: moved 'libxau6_1%3a1.0.11-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpskbr_bx3/libxau6_1.0.11-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-2+b2 [621 kB] Fetched 621 kB in 0s (29.0 MB/s) dpkg-name: info: moved 'libgmp-dev_2%3a6.3.0+dfsg-2+b2_arm64.deb' to '/srv/rebuilderd/tmp/tmp0_o72g3h/libgmp-dev_6.3.0+dfsg-2+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Fetched 388 kB in 0s (17.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkh6p0slb/libssh2-1-dev_1.11.1-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpcre2-8-0 arm64 10.44-4 [243 kB] Fetched 243 kB in 0s (12.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsewc1sz3/libpcre2-8-0_10.44-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libubsan1 arm64 14.2.0-8 [1039 kB] Fetched 1039 kB in 0s (41.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj9iu1w4p/libubsan1_14.2.0-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpcre2-dev arm64 10.44-4 [704 kB] Fetched 704 kB in 0s (30.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnah2mlad/libpcre2-dev_10.44-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libaudit-common all 1:4.0.2-2 [12.7 kB] Fetched 12.7 kB in 0s (696 kB/s) dpkg-name: info: moved 'libaudit-common_1%3a4.0.2-2_all.deb' to '/srv/rebuilderd/tmp/tmptfydc6gd/libaudit-common_4.0.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Fetched 213 kB in 0s (11.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe26uknyn/python3-pkg-resources_75.2.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 fontconfig arm64 2.15.0-1.1+b1 [463 kB] Fetched 463 kB in 0s (22.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyyx3ma1f/fontconfig_2.15.0-1.1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB] Fetched 27.2 kB in 0s (1646 kB/s) dpkg-name: info: moved 'libxrender1_1%3a0.9.10-1.1+b2_arm64.deb' to '/srv/rebuilderd/tmp/tmpispte3hn/libxrender1_0.9.10-1.1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 dwz arm64 0.15-1+b1 [102 kB] Fetched 102 kB in 0s (5909 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5lgyk2fp/dwz_0.15-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libattr1 arm64 1:2.5.2-2 [22.5 kB] Fetched 22.5 kB in 0s (1786 kB/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-2_arm64.deb' to '/srv/rebuilderd/tmp/tmpuy9acuyo/libattr1_2.5.2-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Fetched 20.0 kB in 0s (1228 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp38iet9t7/libsasl2-modules-db_2.1.28+dfsg1-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libmpfr6 arm64 4.2.1-1+b2 [680 kB] Fetched 680 kB in 0s (30.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8zz1u_jp/libmpfr6_4.2.1-1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 sysvinit-utils arm64 3.11-1 [33.0 kB] Fetched 33.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp94ei_bqr/sysvinit-utils_3.11-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Fetched 19.5 kB in 0s (1205 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzpbkzkd1/libfile-stripnondeterminism-perl_1.14.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 openssl arm64 3.3.2-2 [1347 kB] Fetched 1347 kB in 0s (48.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnevrzh5s/openssl_3.3.2-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Fetched 49.3 kB in 0s (2718 kB/s) dpkg-name: info: moved 'libxext6_2%3a1.3.4-1+b2_arm64.deb' to '/srv/rebuilderd/tmp/tmp2y3k1s2_/libxext6_1.3.4-1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libcurl4-gnutls-dev arm64 8.11.0-1 [459 kB] Fetched 459 kB in 0s (21.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_hw_pbar/libcurl4-gnutls-dev_8.11.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 docbook-xml all 4.5-13 [77.4 kB] Fetched 77.4 kB in 0s (4485 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzbjgkt4x/docbook-xml_4.5-13_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Fetched 122 kB in 0s (6919 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmyjwfgej/libidn2-dev_2.3.7-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libssl3t64 arm64 3.3.2-2 [2600 kB] Fetched 2600 kB in 0s (84.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsg09yxfc/libssl3t64_3.3.2-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 binutils-common arm64 2.43.1-5 [2631 kB] Fetched 2631 kB in 0s (69.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfhzj2rr5/binutils-common_2.43.1-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libzstd-dev arm64 1.5.6+dfsg-1+b1 [329 kB] Fetched 329 kB in 0s (16.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp61zfcx8k/libzstd-dev_1.5.6+dfsg-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Fetched 30.4 kB in 0s (1807 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7_y3waw0/libjbig0_2.1-6.1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Fetched 1129 kB in 0s (43.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoo16lpoe/groff-base_1.23.0-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-base-core arm64 4.4.2-1 [28.0 MB] Fetched 28.0 MB in 0s (142 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppawv586j/r-base-core_4.4.2-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Fetched 1812 kB in 0s (57.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8i7p17i6/liblapack3_3.12.0-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-cran-fansi arm64 1.0.5-1+b1 [626 kB] Fetched 626 kB in 0s (29.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptu7e8ejw/r-cran-fansi_1.0.5-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libxrender-dev arm64 1:0.9.10-1.1+b2 [35.7 kB] Fetched 35.7 kB in 0s (2170 kB/s) dpkg-name: info: moved 'libxrender-dev_1%3a0.9.10-1.1+b2_arm64.deb' to '/srv/rebuilderd/tmp/tmpvkweqpoo/libxrender-dev_0.9.10-1.1+b2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxdmcp-dev arm64 1:1.1.5-1 [44.2 kB] Fetched 44.2 kB in 0s (2606 kB/s) dpkg-name: info: moved 'libxdmcp-dev_1%3a1.1.5-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpmp6mccu_/libxdmcp-dev_1.1.5-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Fetched 112 kB in 0s (8436 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppt8x4erq/libsharpyuv0_1.4.0-0.1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libcurl3t64-gnutls arm64 8.11.0-1 [331 kB] Fetched 331 kB in 0s (17.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptvx4vr2t/libcurl3t64-gnutls_8.11.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libkadm5srv-mit12 arm64 1.21.3-3 [52.2 kB] Fetched 52.2 kB in 0s (3125 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1jz8vt8r/libkadm5srv-mit12_1.21.3-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Fetched 71.3 kB in 0s (4248 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8zvvsb45/libnghttp2-14_1.64.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libjson-c5 arm64 0.18+ds-1 [45.2 kB] Fetched 45.2 kB in 0s (2696 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeyto7mdh/libjson-c5_0.18+ds-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libatomic1 arm64 14.2.0-8 [10.1 kB] Fetched 10.1 kB in 0s (611 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0410ggk9/libatomic1_14.2.0-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-3 [33.5 kB] Fetched 33.5 kB in 0s (1964 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbw7uiz4x/libpangocairo-1.0-0_1.54.0+ds-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libglib2.0-0t64 arm64 2.82.2-3 [1411 kB] Fetched 1411 kB in 0s (50.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc_lrbf44/libglib2.0-0t64_2.82.2-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 linux-libc-dev all 6.11.9-1 [2459 kB] Fetched 2459 kB in 0s (68.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9g82jim0/linux-libc-dev_6.11.9-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Fetched 62.3 kB in 0s (3703 kB/s) dpkg-name: info: moved 'libproc2-0_2%3a4.0.4-6_arm64.deb' to '/srv/rebuilderd/tmp/tmp5exo0wt9/libproc2-0_4.0.4-6_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-cran-nlme arm64 3.1.166-1 [2326 kB] Fetched 2326 kB in 0s (66.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkeywd05g/r-cran-nlme_3.1.166-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpaper-utils arm64 1.1.29+b2 [9128 B] Fetched 9128 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcd3w3h48/libpaper-utils_1.1.29+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libtsl-hopscotch-map-dev all 2.3.1-1 [36.6 kB] Fetched 36.6 kB in 0s (2223 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7h6zd770/libtsl-hopscotch-map-dev_2.3.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 procps arm64 2:4.0.4-6 [872 kB] Fetched 872 kB in 0s (36.5 MB/s) dpkg-name: info: moved 'procps_2%3a4.0.4-6_arm64.deb' to '/srv/rebuilderd/tmp/tmp_4h9nuqu/procps_4.0.4-6_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libdebuginfod1t64 arm64 0.192-4 [31.3 kB] Fetched 31.3 kB in 0s (1855 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwqn21apw/libdebuginfod1t64_0.192-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Fetched 80.8 kB in 0s (4803 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx316ff1v/libk5crypto3_1.21.3-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libtsan2 arm64 14.2.0-8 [2386 kB] Fetched 2386 kB in 0s (66.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp_riedf9/libtsan2_14.2.0-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libssw-dev arm64 1.1-15+b1 [23.4 kB] Fetched 23.4 kB in 0s (1411 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbcot6s8p/libssw-dev_1.1-15+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libxml2-dev arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [751 kB] Fetched 751 kB in 0s (34.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpylkf_5b5/libxml2-dev_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-labeling all 0.4.3-1 [62.4 kB] Fetched 62.4 kB in 0s (3716 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpibdgszq6/r-cran-labeling_0.4.3-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 bzip2 arm64 1.0.8-6 [39.5 kB] Fetched 39.5 kB in 0s (2288 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzd_pi8j0/bzip2_1.0.8-6_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8 [10.1 MB] Fetched 10.1 MB in 0s (116 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsfyr1187/g++-14-aarch64-linux-gnu_14.2.0-8_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Fetched 226 kB in 0s (12.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2qbjtnxf/r-cran-withr_3.0.2+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 init-system-helpers all 1.67 [38.7 kB] Fetched 38.7 kB in 0s (3723 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxdahf3qt/init-system-helpers_1.67_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB] Fetched 446 kB in 0s (22.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_rms9huh/libgnutls-openssl27t64_3.8.8-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libonig5 arm64 6.9.9-1+b1 [181 kB] Fetched 181 kB in 0s (10.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsagksm1j/libonig5_6.9.9-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpython3.12-stdlib arm64 3.12.7-3 [1902 kB] Fetched 1902 kB in 0s (59.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo4lk3l0y/libpython3.12-stdlib_3.12.7-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 base-passwd arm64 3.6.5 [52.8 kB] Fetched 52.8 kB in 0s (3167 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpghzhz12j/base-passwd_3.6.5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libstdc++6 arm64 14.2.0-8 [637 kB] Fetched 637 kB in 0s (29.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm8s_sr99/libstdc++6_14.2.0-8_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxcb1-dev arm64 1.17.0-2+b1 [182 kB] Fetched 182 kB in 0s (10.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4j8r_vmd/libxcb1-dev_1.17.0-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxcb-render0-dev arm64 1.17.0-2+b1 [119 kB] Fetched 119 kB in 0s (6943 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp58vi1f6e/libxcb-render0-dev_1.17.0-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libctf0 arm64 2.43.1-5 [84.0 kB] Fetched 84.0 kB in 0s (4892 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgp0f4z22/libctf0_2.43.1-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Fetched 323 kB in 0s (16.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpitg7hhah/libarchive13t64_3.7.4-1.1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1 [1440 B] Fetched 1440 B in 0s (86.6 kB/s) dpkg-name: info: moved 'gcc-aarch64-linux-gnu_4%3a14.2.0-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpg_qjdgjn/gcc-aarch64-linux-gnu_14.2.0-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-3+b1 [49.6 kB] Fetched 49.6 kB in 0s (2911 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpynu6ijtd/liblzo2-2_2.10-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB] Fetched 143 kB in 0s (7915 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpes3k5ogb/libexpat1-dev_2.6.4-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libraptor2-0 arm64 2.0.16-4+b1 [164 kB] Fetched 164 kB in 0s (9135 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr7kpe4e_/libraptor2-0_2.0.16-4+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [982 kB] Fetched 982 kB in 0s (40.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3untcv3f/libtcl8.6_8.6.15+dfsg-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 gettext arm64 0.22.5-2 [1532 kB] Fetched 1532 kB in 0s (53.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo_u8d4xj/gettext_0.22.5-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 liblz4-1 arm64 1.9.4-3+b1 [55.8 kB] Fetched 55.8 kB in 0s (3177 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg02vltm0/liblz4-1_1.9.4-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 docbook-to-man arm64 1:2.0.0-47+b1 [71.4 kB] Fetched 71.4 kB in 0s (4067 kB/s) dpkg-name: info: moved 'docbook-to-man_1%3a2.0.0-47+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmp7mv_4gi8/docbook-to-man_2.0.0-47+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 comerr-dev arm64 2.1-1.47.1-1+b1 [55.1 kB] Fetched 55.1 kB in 0s (3227 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpquol4qp5/comerr-dev_2.1-1.47.1-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libtool all 2.4.7-8 [517 kB] Fetched 517 kB in 0s (25.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg2kx2z12/libtool_2.4.7-8_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgomp1 arm64 14.2.0-8 [124 kB] Fetched 124 kB in 0s (7122 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk50mf_i8/libgomp1_14.2.0-8_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Fetched 32.4 kB in 0s (2035 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpptb3sb4v/python3-inflect_7.3.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1 [4832 B] Fetched 4832 B in 0s (450 kB/s) dpkg-name: info: moved 'cpp-aarch64-linux-gnu_4%3a14.2.0-1_arm64.deb' to '/srv/rebuilderd/tmp/tmp_sw9x3m5/cpp-aarch64-linux-gnu_14.2.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 mawk arm64 1.3.4.20240905-1 [131 kB] Fetched 131 kB in 0s (7661 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv91i5c90/mawk_1.3.4.20240905-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Fetched 42.2 kB in 0s (2453 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppqlr34cx/libdeflate0_1.22-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Fetched 98.0 kB in 0s (5456 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpow2yqt2g/rapidjson-dev_1.1.0+dfsg2-7.3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Fetched 37.6 kB in 0s (2228 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv9nzqp_u/libdatrie1_0.2.13-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgssrpc4t64 arm64 1.21.3-3 [56.7 kB] Fetched 56.7 kB in 0s (3258 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpacicb1zi/libgssrpc4t64_1.21.3-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libdw1t64 arm64 0.192-4 [237 kB] Fetched 237 kB in 0s (12.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu03r3rsg/libdw1t64_0.192-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libsm-dev arm64 2:1.2.4-1 [38.0 kB] Fetched 38.0 kB in 0s (2299 kB/s) dpkg-name: info: moved 'libsm-dev_2%3a1.2.4-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpr5ges0zz/libsm-dev_1.2.4-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libcc1-0 arm64 14.2.0-8 [42.2 kB] Fetched 42.2 kB in 0s (2568 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2juub79g/libcc1-0_14.2.0-8_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1713 kB] Fetched 1713 kB in 0s (55.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0apjk_sc/r-cran-colorspace_2.1-1+dfsg-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Fetched 76.8 kB in 0s (4353 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp589vtnmt/libsparsehash-dev_2.0.3-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libprotoc-dev arm64 3.21.12-10+b1 [937 kB] Fetched 937 kB in 0s (39.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwg_4m5kl/libprotoc-dev_3.21.12-10+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Fetched 10.9 kB in 0s (796 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx6dg1iy5/libtirpc-common_1.3.4+ds-1.3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 ncurses-base all 6.5-2 [270 kB] Fetched 270 kB in 0s (14.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8j0dkavh/ncurses-base_6.5-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 gawk arm64 1:5.2.1-2+b2 [644 kB] Fetched 644 kB in 0s (30.0 MB/s) dpkg-name: info: moved 'gawk_1%3a5.2.1-2+b2_arm64.deb' to '/srv/rebuilderd/tmp/tmp72a84vyq/gawk_5.2.1-2+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Fetched 40.2 kB in 0s (2749 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzqrqhtkp/libpipeline1_1.5.8-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgcrypt20 arm64 1.11.0-6 [741 kB] Fetched 741 kB in 0s (32.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz1iaw3ox/libgcrypt20_1.11.0-6_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Fetched 96.1 kB in 0s (5377 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph77303rw/libncurses6_6.5-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 bwa arm64 0.7.18-1 [198 kB] Fetched 198 kB in 0s (10.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp063m8330/bwa_0.7.18-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 jq arm64 1.7.1-3+b1 [77.3 kB] Fetched 77.3 kB in 0s (5246 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp32es6ou4/jq_1.7.1-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libsystemd0 arm64 257~rc2-3 [416 kB] Fetched 416 kB in 0s (24.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpss1dw9nu/libsystemd0_257~rc2-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 ncurses-bin arm64 6.5-2+b1 [428 kB] Fetched 428 kB in 0s (21.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjdfx09re/ncurses-bin_6.5-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libffi-dev arm64 3.4.6-1 [57.0 kB] Fetched 57.0 kB in 0s (3345 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjcwas3ue/libffi-dev_3.4.6-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Fetched 297 kB in 0s (15.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9b92c865/libbrotli1_1.1.0-2+b6_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-farver arm64 2.1.2-1+b1 [1397 kB] Fetched 1397 kB in 0s (50.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_qtdz4jm/r-cran-farver_2.1.2-1+b1_arm64.deb' Downloading dependency 258 of 475: samtools:arm64=1.20-3+b1 Downloading dependency 259 of 475: libxt6t64:arm64=1:1.2.1-1.2+b1 Downloading dependency 260 of 475: libbackward-cpp-dev:arm64=1.6-1 Downloading dependency 261 of 475: libcrypt-dev:arm64=1:4.4.36-5 Downloading dependency 262 of 475: xz-utils:arm64=5.6.3-1+b1 Downloading dependency 263 of 475: r-cran-gridbase:arm64=0.4-7-5 Downloading dependency 264 of 475: r-cran-pkgconfig:arm64=2.0.3-2 Downloading dependency 265 of 475: libxslt1.1:arm64=1.1.35-1.1+b1 Downloading dependency 266 of 475: autoconf:arm64=2.72-3 Downloading dependency 267 of 475: libpixman-1-0:arm64=0.44.0-3 Downloading dependency 268 of 475: sed:arm64=4.9-2+b1 Downloading dependency 269 of 475: libdisorder-dev:arm64=0.0.2+git20130809.8062ee1-4+b2 Downloading dependency 270 of 475: libffi8:arm64=3.4.6-1 Downloading dependency 271 of 475: libkdb5-10t64:arm64=1.21.3-3 Downloading dependency 272 of 475: libhtscodecs2:arm64=1.6.1-1 Downloading dependency 273 of 475: libnettle8t64:arm64=3.10-1+b1 Downloading dependency 274 of 475: util-linux:arm64=2.40.2-11 Downloading dependency 275 of 475: autopoint:arm64=0.22.5-2 Downloading dependency 276 of 475: libkrb5-3:arm64=1.21.3-3 Downloading dependency 277 of 475: libsm6:arm64=2:1.2.4-1 Downloading dependency 278 of 475: libhwasan0:arm64=14.2.0-8 Downloading dependency 279 of 475: x11-common:arm64=1:7.7+23.1 Downloading dependency 280 of 475: fonts-dejavu-core:arm64=2.37-8 Downloading dependency 281 of 475: libboost-program-options1.83.0:arm64=1.83.0-3.2+b1 Downloading dependency 282 of 475: r-cran-utf8:arm64=1.2.4-1+b1 Downloading dependency 283 of 475: libwfa2-0:arm64=2.3.3-4+b1 Downloading dependency 284 of 475: libxau6:arm64=1:1.0.11-1 Downloading dependency 285 of 475: libgmp-dev:arm64=2:6.3.0+dfsg-2+b2 Downloading dependency 286 of 475: libssh2-1-dev:arm64=1.11.1-1 Downloading dependency 287 of 475: libpcre2-8-0:arm64=10.44-4 Downloading dependency 288 of 475: libubsan1:arm64=14.2.0-8 Downloading dependency 289 of 475: libpcre2-dev:arm64=10.44-4 Downloading dependency 290 of 475: libaudit-common:arm64=1:4.0.2-2 Downloading dependency 291 of 475: python3-pkg-resources:arm64=75.2.0-1 Downloading dependency 292 of 475: fontconfig:arm64=2.15.0-1.1+b1 Downloading dependency 293 of 475: libxrender1:arm64=1:0.9.10-1.1+b2 Downloading dependency 294 of 475: dwz:arm64=0.15-1+b1 Downloading dependency 295 of 475: libattr1:arm64=1:2.5.2-2 Downloading dependency 296 of 475: libsasl2-modules-db:arm64=2.1.28+dfsg1-8 Downloading dependency 297 of 475: libmpfr6:arm64=4.2.1-1+b2 Downloading dependency 298 of 475: sysvinit-utils:arm64=3.11-1 Downloading dependency 299 of 475: libfile-stripnondeterminism-perl:arm64=1.14.0-1 Downloading dependency 300 of 475: openssl:arm64=3.3.2-2 Downloading dependency 301 of 475: libxext6:arm64=2:1.3.4-1+b2 Downloading dependency 302 of 475: libcurl4-gnutls-dev:arm64=8.11.0-1 Downloading dependency 303 of 475: docbook-xml:arm64=4.5-13 Downloading dependency 304 of 475: libidn2-dev:arm64=2.3.7-2+b1 Downloading dependency 305 of 475: libssl3t64:arm64=3.3.2-2 Downloading dependency 306 of 475: binutils-common:arm64=2.43.1-5 Downloading dependency 307 of 475: libzstd-dev:arm64=1.5.6+dfsg-1+b1 Downloading dependency 308 of 475: libjbig0:arm64=2.1-6.1+b2 Downloading dependency 309 of 475: groff-base:arm64=1.23.0-5 Downloading dependency 310 of 475: r-base-core:arm64=4.4.2-1 Downloading dependency 311 of 475: liblapack3:arm64=3.12.0-4 Downloading dependency 312 of 475: r-cran-fansi:arm64=1.0.5-1+b1 Downloading dependency 313 of 475: libxrender-dev:arm64=1:0.9.10-1.1+b2 Downloading dependency 314 of 475: libxdmcp-dev:arm64=1:1.1.5-1 Downloading dependency 315 of 475: libsharpyuv0:arm64=1.4.0-0.1+b1 Downloading dependency 316 of 475: libcurl3t64-gnutls:arm64=8.11.0-1 Downloading dependency 317 of 475: libkadm5srv-mit12:arm64=1.21.3-3 Downloading dependency 318 of 475: libnghttp2-14:arm64=1.64.0-1 Downloading dependency 319 of 475: libjson-c5:arm64=0.18+ds-1 Downloading dependency 320 of 475: libatomic1:arm64=14.2.0-8 Downloading dependency 321 of 475: libpangocairo-1.0-0:arm64=1.54.0+ds-3 Downloading dependency 322 of 475: libglib2.0-0t64:arm64=2.82.2-3 Downloading dependency 323 of 475: linux-libc-dev:arm64=6.11.9-1 Downloading dependency 324 of 475: libproc2-0:arm64=2:4.0.4-6 Downloading dependency 325 of 475: r-cran-nlme:arm64=3.1.166-1 Downloading dependency 326 of 475: libpaper-utils:arm64=1.1.29+b2 Downloading dependency 327 of 475: libtsl-hopscotch-map-dev:arm64=2.3.1-1 Downloading dependency 328 of 475: procps:arm64=2:4.0.4-6 Downloading dependency 329 of 475: libdebuginfod1t64:arm64=0.192-4 Downloading dependency 330 of 475: libk5crypto3:arm64=1.21.3-3 Downloading dependency 331 of 475: libtsan2:arm64=14.2.0-8 Downloading dependency 332 of 475: libssw-dev:arm64=1.1-15+b1 Downloading dependency 333 of 475: libxml2-dev:arm64=2.12.7+dfsg+really2.9.14-0.2+b1 Downloading dependency 334 of 475: r-cran-labeling:arm64=0.4.3-1 Downloading dependency 335 of 475: bzip2:arm64=1.0.8-6 Downloading dependency 336 of 475: g++-14-aarch64-linux-gnu:arm64=14.2.0-8 Downloading dependency 337 of 475: r-cran-withr:arm64=3.0.2+dfsg-1 Downloading dependency 338 of 475: init-system-helpers:arm64=1.67 Downloading dependency 339 of 475: libgnutls-openssl27t64:arm64=3.8.8-2 Downloading dependency 340 of 475: libonig5:arm64=6.9.9-1+b1 Downloading dependency 341 of 475: libpython3.12-stdlib:arm64=3.12.7-3 Downloading dependency 342 of 475: base-passwd:arm64=3.6.5 Downloading dependency 343 of 475: libstdc++6:arm64=14.2.0-8 Downloading dependency 344 of 475: libxcb1-dev:arm64=1.17.0-2+b1 Downloading dependency 345 of 475: libxcb-render0-dev:arm64=1.17.0-2+b1 Downloading dependency 346 of 475: libctf0:arm64=2.43.1-5 Downloading dependency 347 of 475: libarchive13t64:arm64=3.7.4-1.1 Downloading dependency 348 of 475: gcc-aarch64-linux-gnu:arm64=4:14.2.0-1 Downloading dependency 349 of 475: liblzo2-2:arm64=2.10-3+b1 Downloading dependency 350 of 475: libexpat1-dev:arm64=2.6.4-1 Downloading dependency 351 of 475: libraptor2-0:arm64=2.0.16-4+b1 Downloading dependency 352 of 475: libtcl8.6:arm64=8.6.15+dfsg-2 Downloading dependency 353 of 475: gettext:arm64=0.22.5-2 Downloading dependency 354 of 475: liblz4-1:arm64=1.9.4-3+b1 Downloading dependency 355 of 475: docbook-to-man:arm64=1:2.0.0-47+b1 Downloading dependency 356 of 475: comerr-dev:arm64=2.1-1.47.1-1+b1 Downloading dependency 357 of 475: libtool:arm64=2.4.7-8 Downloading dependency 358 of 475: libgomp1:arm64=14.2.0-8 Downloading dependency 359 of 475: python3-inflect:arm64=7.3.1-2 Downloading dependency 360 of 475: cpp-aarch64-linux-gnu:arm64=4:14.2.0-1 Downloading dependency 361 of 475: mawk:arm64=1.3.4.20240905-1 Downloading dependency 362 of 475: libdeflate0:arm64=1.22-1 Downloading dependency 363 of 475: rapidjson-dev:arm64=1.1.0+dfsg2-7.3 Downloading dependency 364 of 475: libdatrie1:arm64=0.2.13-3+b1 Downloading dependency 365 of 475: libgssrpc4t64:arm64=1.21.3-3 Downloading dependency 366 of 475: libdw1t64:arm64=0.192-4 Downloading dependency 367 of 475: libsm-dev:arm64=2:1.2.4-1 Downloading dependency 368 of 475: libcc1-0:arm64=14.2.0-8 Downloading dependency 369 of 475: r-cran-colorspace:arm64=2.1-1+dfsg-1 Downloading dependency 370 of 475: libsparsehash-dev:arm64=2.0.3-2 Downloading dependency 371 of 475: libprotoc-dev:arm64=3.21.12-10+b1 Downloading dependency 372 of 475: libtirpc-common:arm64=1.3.4+ds-1.3 Downloading dependency 373 of 475: ncurses-base:arm64=6.5-2 Downloading dependency 374 of 475: gawk:arm64=1:5.2.1-2+b2 Downloading dependency 375 of 475: libpipeline1:arm64=1.5.8-1 Downloading dependency 376 of 475: libgcrypt20:arm64=1.11.0-6 Downloading dependency 377 of 475: libncurses6:arm64=6.5-2+b1 Downloading dependency 378 of 475: bwa:arm64=0.7.18-1 Downloading dependency 379 of 475: jq:arm64=1.7.1-3+b1 Downloading dependency 380 of 475: libsystemd0:arm64=257~rc2-3 Downloading dependency 381 of 475: ncurses-bin:arm64=6.5-2+b1 Downloading dependency 382 of 475: libffi-dev:arm64=3.4.6-1 Downloading dependency 383 of 475: libbrotli1:arm64=1.1.0-2+b6 Downloading dependency 384 of 475: r-cran-farver:arm64=2.1.2-1+b1 Downloading dependency 385 of 475: libfontconfig1:arm64=2.15.0-1.1+b1Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Fetched 387 kB in 0s (19.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx5qzkc2m/libfontconfig1_2.15.0-1.1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 media-types all 10.1.0 [26.9 kB] Fetched 26.9 kB in 0s (1610 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1o4pbvu7/media-types_10.1.0_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libvcflib-dev arm64 1.0.9+dfsg1-3+b2 [77.8 kB] Fetched 77.8 kB in 0s (4589 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd_xceubt/libvcflib-dev_1.0.9+dfsg1-3+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libkadm5clnt-mit12 arm64 1.21.3-3 [40.3 kB] Fetched 40.3 kB in 0s (3219 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvl1zvulm/libkadm5clnt-mit12_1.21.3-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libtabixpp0t64 arm64 1.1.2-2.1+b1 [9504 B] Fetched 9504 B in 0s (537 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_xl4ben_/libtabixpp0t64_1.1.2-2.1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Fetched 268 kB in 0s (14.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp52rp7fkx/libwebp7_1.4.0-0.1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libfastahack0 arm64 1.0.0+dfsg-11+b2 [23.6 kB] Fetched 23.6 kB in 0s (1383 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplqliy_jr/libfastahack0_1.0.0+dfsg-11+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 zip arm64 3.0-14+b1 [227 kB] Fetched 227 kB in 0s (12.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd42q6you/zip_3.0-14+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libc6-dev arm64 2.40-3 [1591 kB] Fetched 1591 kB in 0s (51.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfxk4qf2i/libc6-dev_2.40-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libjq1 arm64 1.7.1-3+b1 [148 kB] Fetched 148 kB in 0s (8288 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpygi7bm62/libjq1_1.7.1-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 debconf all 1.5.87 [119 kB] Fetched 119 kB in 0s (6592 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbs7ekusv/debconf_1.5.87_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 coreutils arm64 9.5-1+b1 [2858 kB] Fetched 2858 kB in 0s (72.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjuphv766/coreutils_9.5-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-3 [51.8 kB] Fetched 51.8 kB in 0s (2872 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe1gfawts/libpangoft2-1.0-0_1.54.0+ds-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Fetched 126 kB in 0s (10.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph4d7oqkq/libgssapi-krb5-2_1.21.3-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 g++ arm64 4:14.2.0-1 [1332 B] Fetched 1332 B in 0s (82.8 kB/s) dpkg-name: info: moved 'g++_4%3a14.2.0-1_arm64.deb' to '/srv/rebuilderd/tmp/tmpmhgvh_rx/g++_14.2.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libp11-kit-dev arm64 0.25.5-2+b1 [208 kB] Fetched 208 kB in 0s (11.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_j6qsrbp/libp11-kit-dev_0.25.5-2+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Fetched 3933 kB in 0s (90.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8yabl7uj/r-cran-ggplot2_3.5.1+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpython3-stdlib arm64 3.12.7-1 [9708 B] Fetched 9708 B in 0s (589 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6x4enswb/libpython3-stdlib_3.12.7-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 rasqal-utils arm64 0.9.33-2.1+b2 [43.1 kB] Fetched 43.1 kB in 0s (2474 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgkxcp8_9/rasqal-utils_0.9.33-2.1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libc6 arm64 2.40-3 [2453 kB] Fetched 2453 kB in 0s (66.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbjk0g4af/libc6_2.40-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Fetched 70.4 kB in 0s (3728 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzew_9rq4/libgraphite2-3_1.3.14-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Fetched 9352 B in 0s (564 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc_o6qcnn/libkeyutils1_1.6.3-4_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libacl1 arm64 2.3.2-2+b1 [32.2 kB] Fetched 32.2 kB in 0s (1891 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpese_3h15/libacl1_2.3.2-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Fetched 55.2 kB in 0s (3210 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo3n0kc7d/ucf_3.0043+nmu1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Fetched 22.9 kB in 0s (1327 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphnhx9ah6/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libssw0 arm64 1.1-15+b1 [20.0 kB] Fetched 20.0 kB in 0s (1147 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwga_ryrs/libssw0_1.1-15+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (6087 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_j18xfim/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Fetched 90.7 kB in 0s (5312 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpio3cdcky/libexpat1_2.6.4-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Fetched 110 kB in 0s (10.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1dxiwfr7/r-cran-lifecycle_1.0.4+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Fetched 67.5 kB in 0s (3929 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuy79r0d0/librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgdbm6t64 arm64 1.24-2 [74.0 kB] Fetched 74.0 kB in 0s (4357 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuargybl6/libgdbm6t64_1.24-2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 base-files arm64 13.5 [72.8 kB] Fetched 72.8 kB in 0s (4335 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvc7jsp3c/base-files_13.5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libvcflib2 arm64 1.0.9+dfsg1-3+b2 [165 kB] Fetched 165 kB in 0s (14.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjoap1z24/libvcflib2_1.0.9+dfsg1-3+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libsqlite3-0 arm64 3.46.1-1 [852 kB] Fetched 852 kB in 0s (35.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsnijir14/libsqlite3-0_3.46.1-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libjansson-dev arm64 2.14-2+b3 [43.6 kB] Fetched 43.6 kB in 0s (2518 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6uwla2wi/libjansson-dev_2.14-2+b3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libkrb5-dev arm64 1.21.3-3 [15.8 kB] Fetched 15.8 kB in 0s (923 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd1t792in/libkrb5-dev_1.21.3-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Fetched 102 kB in 0s (5691 kB/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.45-3+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmplyowuz29/libmagic1t64_5.45-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Fetched 32.1 kB in 0s (1867 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfh44ehd_/libkrb5support0_1.21.3-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libjemalloc2 arm64 5.3.0-2+b2 [217 kB] Fetched 217 kB in 0s (11.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_zemmkap/libjemalloc2_5.3.0-2+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 krb5-multidev arm64 1.21.3-3 [126 kB] Fetched 126 kB in 0s (7075 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnixq9o4o/krb5-multidev_1.21.3-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Fetched 337 kB in 0s (16.6 MB/s) dpkg-name: info: moved 'libx11-data_2%3a1.8.10-2_all.deb' to '/srv/rebuilderd/tmp/tmpybysm1kc/libx11-data_1.8.10-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libblkid-dev arm64 2.40.2-11 [208 kB] Fetched 208 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj0hnvby3/libblkid-dev_2.40.2-11_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpixman-1-dev arm64 0.44.0-3 [11.4 kB] Fetched 11.4 kB in 0s (724 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5027qh6o/libpixman-1-dev_0.44.0-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libsframe1 arm64 2.43.1-5 [76.5 kB] Fetched 76.5 kB in 0s (4602 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqz97emsg/libsframe1_2.43.1-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libasm1t64 arm64 0.192-4 [28.2 kB] Fetched 28.2 kB in 0s (1963 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqq24q6z5/libasm1t64_0.192-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Fetched 3185 kB in 0s (75.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpama038s9/libssl-dev_3.3.2-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Fetched 29.6 kB in 0s (1773 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzoh7rhbr/pkgconf-bin_1.8.1-4_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Fetched 73.0 kB in 0s (4292 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpneq32kzn/python3-typing-extensions_4.12.2-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Fetched 20.1 kB in 0s (1206 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqp5tunub/xml-core_0.19_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1 [1200 B] Fetched 1200 B in 0s (74.4 kB/s) dpkg-name: info: moved 'g++-aarch64-linux-gnu_4%3a14.2.0-1_arm64.deb' to '/srv/rebuilderd/tmp/tmplrzbgnzo/g++-aarch64-linux-gnu_14.2.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Fetched 1324 kB in 0s (48.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa18zh76t/nettle-dev_3.10-1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Fetched 422 kB in 0s (20.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp86_j4x9k/libfreetype6_2.13.3+dfsg-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 icu-devtools arm64 72.1-5+b1 [195 kB] Fetched 195 kB in 0s (10.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5tm3nnn8/icu-devtools_72.1-5+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libudev1 arm64 257~rc2-3 [139 kB] Fetched 139 kB in 0s (7627 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5z59y7rb/libudev1_257~rc2-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libboost-program-options1.83-dev arm64 1.83.0-3.2+b1 [369 kB] Fetched 369 kB in 0s (18.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaojd5mn_/libboost-program-options1.83-dev_1.83.0-3.2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 girepository-tools arm64 2.82.2-3 [134 kB] Fetched 134 kB in 0s (7656 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpar0f12f1/girepository-tools_2.82.2-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Fetched 54.7 kB in 0s (3212 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt1w50cze/r-cran-rcolorbrewer_1.1-3-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Fetched 71.8 kB in 0s (3959 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq8a6yejm/libfribidi0_1.0.15-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libglib2.0-bin arm64 2.82.2-3 [123 kB] Fetched 123 kB in 0s (6914 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3as9q0at/libglib2.0-bin_2.82.2-3_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgirepository-2.0-0 arm64 2.82.2-3 [130 kB] Fetched 130 kB in 0s (7358 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpselk5ru5/libgirepository-2.0-0_2.82.2-3_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Fetched 15.2 kB in 0s (910 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk08z1grw/liblocale-gettext-perl_1.07-7+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libblkid1 arm64 2.40.2-11 [162 kB] Fetched 162 kB in 0s (9094 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9v0obhl6/libblkid1_2.40.2-11_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 librasqal3t64 arm64 0.9.33-2.1+b2 [178 kB] Fetched 178 kB in 0s (9455 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpliseyge2/librasqal3t64_0.9.33-2.1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libbinutils arm64 2.43.1-5 [657 kB] Fetched 657 kB in 0s (30.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1w_erud5/libbinutils_2.43.1-5_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Fetched 105 kB in 0s (8640 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmiw2mje1/libxcb-shm0_1.17.0-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Fetched 9239 kB in 0s (109 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpelh3lvv4/libicu72_72.1-5+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Fetched 917 kB in 0s (37.5 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb' to '/srv/rebuilderd/tmp/tmpktud_95w/zlib1g-dev_1.3.dfsg+really1.3.1-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libfml-dev arm64 0.1+git20190320.b499514-1+b2 [80.0 kB] Fetched 80.0 kB in 0s (4652 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzcg4n23x/libfml-dev_0.1+git20190320.b499514-1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 r-cran-mgcv arm64 1.9-1-1+b1 [3218 kB] Fetched 3218 kB in 0s (75.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp01w5m2a3/r-cran-mgcv_1.9-1-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 perl arm64 5.40.0-7 [267 kB] Fetched 267 kB in 0s (13.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw31fix1k/perl_5.40.0-7_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 littler all 0.3.20-1 [16.0 kB] Fetched 16.0 kB in 0s (967 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe9kmzu0p/littler_0.3.20-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libyajl-dev arm64 2.1.0-5+b2 [31.0 kB] Fetched 31.0 kB in 0s (1754 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp_iamr76/libyajl-dev_2.1.0-5+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 bash arm64 5.2.32-1+b2 [1453 kB] Fetched 1453 kB in 0s (51.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvnzt5o4e/bash_5.2.32-1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 man-db arm64 2.13.0-1 [1404 kB] Fetched 1404 kB in 0s (50.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf7btnnl6/man-db_2.13.0-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 grep arm64 3.11-4+b1 [426 kB] Fetched 426 kB in 0s (20.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpezlj43f4/grep_3.11-4+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 x11proto-core-dev all 2024.1-1 [3312 B] Fetched 3312 B in 0s (194 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaae8b3wg/x11proto-core-dev_2024.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libpam-modules-bin arm64 1.5.3-7+b1 [53.8 kB] Fetched 53.8 kB in 0s (3158 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkl1vdp44/libpam-modules-bin_1.5.3-7+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libisl23 arm64 0.27-1 [601 kB] Fetched 601 kB in 0s (27.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphkjo0hre/libisl23_0.27-1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Fetched 483 kB in 0s (23.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7tc7znx7/libcairo2_1.18.2-2_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Fetched 146 kB in 0s (8156 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_862yzt5/liblerc4_4.0.0+ds-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 tar arm64 1.35+dfsg-3+b1 [803 kB] Fetched 803 kB in 0s (34.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdpxx6hn9/tar_1.35+dfsg-3+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libtinfo6 arm64 6.5-2+b1 [337 kB] Fetched 337 kB in 0s (17.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptdnixn1n/libtinfo6_6.5-2+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libfml0 arm64 0.1+git20190320.b499514-1+b2 [65.9 kB] Fetched 65.9 kB in 0s (3733 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2lpctkhh/libfml0_0.1+git20190320.b499514-1+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 sgml-base all 1.31 [15.4 kB] Fetched 15.4 kB in 0s (865 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuj447fu9/sgml-base_1.31_all.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libfastahack-dev arm64 1.0.0+dfsg-11+b2 [26.1 kB] Fetched 26.1 kB in 0s (1582 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeiehnnyj/libfastahack-dev_1.0.0+dfsg-11+b2_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libdeflate-dev arm64 1.22-1 [51.2 kB] Fetched 51.2 kB in 0s (3035 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpofwzkqpo/libdeflate-dev_1.22-1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Fetched 170 kB in 0s (9160 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0nusm9sj/libevent-2.1-7t64_2.1.12-stable-10+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libgprofng0 arm64 2.43.1-5 [690 kB] Fetched 690 kB in 0s (52.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx2_2vef5/libgprofng0_2.43.1-5_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 libxslt1-dev arm64 1.1.35-1.1+b1 [345 kB] Fetched 345 kB in 0s (16.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3uk91mxb/libxslt1-dev_1.1.35-1.1+b1_arm64.deb' Get:1 http://deb.debian.org/debian unstable/main arm64 r-cran-isoband arm64 0.2.7-1+b1 [1614 kB] Fetched 1614 kB in 0s (52.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2_kdz190/r-cran-isoband_0.2.7-1+b1_arm64.deb' Get:1 http://snapshot.debian.org/archive/debian/20241122T143055Z sid/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8 [17.7 MB] Fetched 17.7 MB in 0s (117 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbs0x24uj/gcc-14-aarch64-linux-gnu_14.2.0-8_arm64.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 arm64 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_arm64.buildinfo dpkg-genchanges --build=binary -O../debootsnap-dummy_1.0_arm64.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/tmp7u9y51lc/cache directory, not in ".." as indicated by the message above! I: automatically chosen mode: unshare I: chroot architecture arm64 is equal to the host's architecture I: using /srv/rebuilderd/tmp/mmdebstrap.dh5ete4z_g as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.dh5ete4z_g 127.0.0.1 - - [27/Nov/2025 13:05:58] code 404, message File not found 127.0.0.1 - - [27/Nov/2025 13:05:58] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:43463 ./ InRelease 127.0.0.1 - - [27/Nov/2025 13:05:58] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:43463 ./ Release [462 B] 127.0.0.1 - - [27/Nov/2025 13:05:58] code 404, message File not found 127.0.0.1 - - [27/Nov/2025 13:05:58] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:43463 ./ Release.gpg 127.0.0.1 - - [27/Nov/2025 13:05:58] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:43463 ./ Packages [600 kB] Fetched 600 kB in 0s (14.8 MB/s) Reading package lists... usr-is-merged found -- running merged-usr setup hook dpkg-deb: building package 'usr-is-merged' in '/srv/rebuilderd/tmp/mmdebstrap.dh5ete4z_g/tmp/tmp.G43PITDBaG/usr-is-merged.deb'. Selecting previously unselected package usr-is-merged. (Reading database ... 0 files and directories currently installed.) Preparing to unpack .../usr-is-merged.deb ... Unpacking usr-is-merged (1) ... touch: cannot touch '/run/needrestart/unpacked': Permission denied Setting up usr-is-merged (1) ... I: skipping apt-get update because it was already run I: downloading packages with apt... 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./gcc-14-base_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libc6_2.40-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libgcc-s1_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./mawk_1.3.4.20240905-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./base-files_13.5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libtinfo6_6.5-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./debianutils_5.21_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./bash_5.2.32-1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libcap2_2.66-5%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libsystemd0_257%7erc2-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./bsdutils_2.40.2-11_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libacl1_2.3.2-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libattr1_2.5.2-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libgmp10_6.3.0%2bdfsg-2%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libpcre2-8-0_10.44-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libselinux1_3.7-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libzstd1_1.5.6%2bdfsg-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./zlib1g_1.3.dfsg%2breally1.3.1-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libssl3t64_3.3.2-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./openssl-provider-legacy_3.3.2-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./coreutils_9.5-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./dash_0.5.12-9%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./diffutils_3.10-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libbz2-1.0_1.0.8-6_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./liblzma5_5.6.3-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libmd0_1.1.0-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./tar_1.35%2bdfsg-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./dpkg_1.22.11_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./findutils_4.10.0-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./grep_3.11-4%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./gzip_1.12-1.1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./hostname_3.25_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./ncurses-bin_6.5-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libcrypt1_4.4.36-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./perl-base_5.40.0-7_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./sed_4.9-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libaudit-common_4.0.2-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libcap-ng0_0.8.5-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libaudit1_4.0.2-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libdb5.3t64_5.3.28%2bdfsg2-9_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./debconf_1.5.87_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libpam0g_1.5.3-7%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libpam-modules-bin_1.5.3-7%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libpam-modules_1.5.3-7%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libpam-runtime_1.5.3-7_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libblkid1_2.40.2-11_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libmount1_2.40.2-11_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libsmartcols1_2.40.2-11_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libudev1_257%7erc2-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libuuid1_2.40.2-11_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./util-linux_2.40.2-11_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libdebconfclient0_0.273_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./base-passwd_3.6.5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./init-system-helpers_1.67_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./libc-bin_2.40-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./ncurses-base_6.5-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:05:59] "GET /./sysvinit-utils_3.11-1_arm64.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.dh5ete4z_g 127.0.0.1 - - [27/Nov/2025 13:06:02] code 404, message File not found 127.0.0.1 - - [27/Nov/2025 13:06:02] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:43463 ./ InRelease 127.0.0.1 - - [27/Nov/2025 13:06:02] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:43463 ./ Release 127.0.0.1 - - [27/Nov/2025 13:06:02] code 404, message File not found 127.0.0.1 - - [27/Nov/2025 13:06:02] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:43463 ./ Release.gpg Reading package lists... usr-is-merged found -- 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.dh5ete4z_g dummy usr-is-merged package installed -- running merged-usr essential hook Reading package lists... Building dependency tree... The following packages will be upgraded: usr-is-merged 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./usr-is-merged_39_all.deb HTTP/1.1" 200 - 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5572 B of archives. After this operation, 13.3 kB of additional disk space will be used. Get:1 http://localhost:43463 ./ usr-is-merged 39 [5572 B] Fetched 5572 B in 0s (303 kB/s) Chrooting into /srv/rebuilderd/tmp/mmdebstrap.dh5ete4z_g/ (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 ... 3540 files and directories currently installed.) Preparing to unpack .../usr-is-merged_39_all.deb ... Unpacking usr-is-merged (39) over (1) ... Chrooting into /srv/rebuilderd/tmp/mmdebstrap.dh5ete4z_g/ Setting up usr-is-merged (39) ... Chrooting into /srv/rebuilderd/tmp/mmdebstrap.dh5ete4z_g/ I: installing remaining packages inside the chroot... 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./liblocale-gettext-perl_1.07-7%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./perl-modules-5.40_5.40.0-7_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libgdbm6t64_1.24-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libgdbm-compat4t64_1.24-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libperl5.40_5.40.0-7_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./perl_5.40.0-7_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./m4_1.4.19-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./flex_2.6.4-8.2%2bb3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libmpfr6_4.2.1-1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./readline-common_8.2-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libreadline8t64_8.2-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libsigsegv2_2.14-1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./gawk_5.2.1-2%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./sensible-utils_0.0.24_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./ucf_3.0043%2bnmu1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libdebuginfod-common_0.192-4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libpython3.12-minimal_3.12.7-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libexpat1_2.6.4-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./python3.12-minimal_3.12.7-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./python3-minimal_3.12.7-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./media-types_10.1.0_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./netbase_6.4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./tzdata_2024b-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libffi8_3.4.6-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libncursesw6_6.5-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libkrb5support0_1.21.3-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libcom-err2_1.47.1-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libk5crypto3_1.21.3-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libkeyutils1_1.6.3-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libkrb5-3_1.21.3-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libgssapi-krb5-2_1.21.3-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libtirpc-common_1.3.4%2bds-1.3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libtirpc3t64_1.3.4%2bds-1.3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libnsl2_1.3.0-3%2bb3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libsqlite3-0_3.46.1-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libpython3.12-stdlib_3.12.7-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./python3.12_3.12.7-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libpython3-stdlib_3.12.7-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./python3_3.12.7-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./sgml-base_1.31_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libstdc%2b%2b6_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libuchardet0_0.0.8-1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./groff-base_1.23.0-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./bsdextrautils_2.40.2-11_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libpipeline1_1.5.8-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libseccomp2_2.5.5-1%2bb3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./man-db_2.13.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libproc2-0_4.0.4-6_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./procps_4.0.4-6_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./bc_1.07.1-4%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./bzip2_1.0.8-6_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./openssl_3.3.2-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./ca-certificates_20240203_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libmagic-mgc_5.45-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libmagic1t64_5.45-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./file_5.45-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./gettext-base_0.22.5-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./xz-utils_5.6.3-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./autoconf_2.72-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./autotools-dev_20220109.1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./automake_1.16.5-1.3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./autopoint_0.22.5-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./binutils-common_2.43.1-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libsframe1_2.43.1-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libbinutils_2.43.1-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libctf-nobfd0_2.43.1-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libctf0_2.43.1-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libgprofng0_2.43.1-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libjansson4_2.14-2%2bb3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./binutils-aarch64-linux-gnu_2.43.1-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./binutils_2.43.1-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./bison_3.8.2%2bdfsg-1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libc-dev-bin_2.40-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./linux-libc-dev_6.11.9-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libcrypt-dev_4.4.36-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./rpcsvc-proto_1.4.3-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libc6-dev_2.40-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libisl23_0.27-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./libmpc3_1.3.1-1%2bb3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:10] "GET /./cpp-14-aarch64-linux-gnu_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./cpp-14_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./cpp-aarch64-linux-gnu_14.2.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./cpp_14.2.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libcc1-0_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libgomp1_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libitm1_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libatomic1_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libasan8_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./liblsan0_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libtsan2_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libubsan1_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libhwasan0_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libgcc-14-dev_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./gcc-14-aarch64-linux-gnu_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./gcc-14_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./gcc-aarch64-linux-gnu_14.2.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./gcc_14.2.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libstdc%2b%2b-14-dev_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./g%2b%2b-14-aarch64-linux-gnu_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./g%2b%2b-14_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./g%2b%2b-aarch64-linux-gnu_14.2.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./g%2b%2b_14.2.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./make_4.3-4.1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libdpkg-perl_1.22.11_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./patch_2.7.6-7%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./dpkg-dev_1.22.11_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./build-essential_12.12_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./bwa_0.7.18-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./cmake-data_3.31.1-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libxxhash0_0.8.2-2%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./liblz4-1_1.9.4-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libnettle8t64_3.10-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libicu72_72.1-5%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libxml2_2.12.7%2bdfsg%2breally2.9.14-0.2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libarchive13t64_3.7.4-1.1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libbrotli1_1.1.0-2%2bb6_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libunistring5_1.2-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libidn2-0_2.3.7-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libhogweed6t64_3.10-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libp11-kit0_0.25.5-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libtasn1-6_4.19.0-3%2bb3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libgnutls30t64_3.8.8-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libsasl2-modules-db_2.1.28%2bdfsg1-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libsasl2-2_2.1.28%2bdfsg1-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libldap-2.5-0_2.5.18%2bdfsg-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libnghttp2-14_1.64.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libpsl5t64_0.21.2-1.1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./librtmp1_2.4%2b20151223.gitfa8646d.1-2%2bb5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libssh2-1t64_1.11.1-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libcurl4t64_8.11.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libjsoncpp26_1.9.6-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./librhash1_1.4.5-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libuv1t64_1.48.0-7_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./cmake_3.31.1-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./comerr-dev_2.1-1.47.1-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libdebhelper-perl_13.20_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libtool_2.4.7-8_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./dh-autoreconf_20_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libarchive-zip-perl_1.68-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libfile-stripnondeterminism-perl_1.14.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./dh-strip-nondeterminism_1.14.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libelf1t64_0.192-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./dwz_0.15-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./gettext_0.22.5-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./intltool-debian_0.35.0%2b20060710.6_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./po-debconf_1.0.21%2bnmu1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./debhelper_13.20_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./native-architecture_0.2.3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./zip_3.0-14%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./unzip_6.0-28%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libpaper1_1.1.29%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libpaper-utils_1.1.29%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./xdg-utils_1.1.3-4.1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libblas3_3.12.0-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libpng16-16t64_1.6.44-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libfreetype6_2.13.3%2bdfsg-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./fonts-dejavu-mono_2.37-8_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./fonts-dejavu-core_2.37-8_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./fontconfig-config_2.15.0-1.1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libfontconfig1_2.15.0-1.1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libpixman-1-0_0.44.0-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libxau6_1.0.11-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libxdmcp6_1.1.5-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libxcb1_1.17.0-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libx11-data_1.8.10-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libx11-6_1.8.10-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libxcb-render0_1.17.0-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libxcb-shm0_1.17.0-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libxext6_1.3.4-1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libxrender1_0.9.10-1.1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libcairo2_1.18.2-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libdeflate0_1.22-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libglib2.0-0t64_2.82.2-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libjpeg62-turbo_2.1.5-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libgfortran5_14.2.0-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./liblapack3_3.12.0-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./fontconfig_2.15.0-1.1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libfribidi0_1.0.15-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libgraphite2-3_1.3.14-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libharfbuzz0b_10.0.1-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libthai-data_0.1.29-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libdatrie1_0.2.13-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libthai0_0.1.29-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libpango-1.0-0_1.54.0%2bds-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libpangoft2-1.0-0_1.54.0%2bds-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libpangocairo-1.0-0_1.54.0%2bds-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libtcl8.6_8.6.15%2bdfsg-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libjbig0_2.1-6.1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./liblerc4_4.0.0%2bds-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libsharpyuv0_1.4.0-0.1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libwebp7_1.4.0-0.1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libtiff6_4.5.1%2bgit230720-5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libxft2_2.3.6-1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./x11-common_7.7%2b23.1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libxss1_1.2.3-1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libtk8.6_8.6.15-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libice6_1.1.1-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libsm6_1.2.4-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./libxt6t64_1.2.1-1.2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:11] "GET /./r-base-core_4.4.2-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-littler_0.3.20-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./liblzma-dev_5.6.3-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libdisorder0_0.0.2%2bgit20130809.8062ee1-4%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libfastahack0_1.0.0%2bdfsg-11%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libsmithwaterman0_0.0%2bgit20160702.2610e25-12%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libnghttp3-9_1.4.0-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libngtcp2-16_1.6.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libngtcp2-crypto-gnutls8_1.6.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libcurl3t64-gnutls_8.11.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libhtscodecs2_1.6.1-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libhts3t64_1.20%2bds-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libtabixpp0t64_1.1.2-2.1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libwfa2-0_2.3.3-4%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libvcflib2_1.0.9%2bdfsg1-3%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./littler_0.3.20-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-pkgkitten_0.2.4-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-rcpp_1.0.13-1-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-plyr_1.8.9-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-cli_3.6.3-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-glue_1.7.0-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-rlang_1.1.4-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-lifecycle_1.0.4%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-gtable_0.3.6%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-isoband_0.2.7-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-mass_7.3-61-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-lattice_0.22-6-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-nlme_3.1.166-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-matrix_1.7-1-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-mgcv_1.9-1-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-farver_2.1.2-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-labeling_0.4.3-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-colorspace_2.1-1%2bdfsg-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-munsell_0.5.1-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-r6_2.5.1-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-rcolorbrewer_1.1-3-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-viridislite_0.4.2-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-scales_1.3.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-fansi_1.0.5-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-magrittr_2.0.3-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-utf8_1.2.4-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-vctrs_0.6.5-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-pillar_1.9.0%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-pkgconfig_2.0.3-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-tibble_3.2.1%2bdfsg-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-withr_3.0.2%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-ggplot2_3.5.1%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./r-cran-gridbase_0.4-7-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libvcflib-tools_1.0.9%2bdfsg1-3%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libcairo-gobject2_1.18.2-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./uuid-dev_2.40.2-11_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./xml-core_0.19_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./sgml-data_2.0.11%2bnmu1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./docbook_4.5-11_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libgpg-error0_1.50-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libjemalloc2_5.3.0-2%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libjemalloc-dev_5.3.0-2%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./python3-packaging_24.2-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libgio-2.0-dev-bin_2.82.2-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./xorg-sgml-doctools_1.11-1.1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./x11proto-dev_2024.1-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libice-dev_1.1.1-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libprotobuf32t64_3.21.12-10%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libprotoc32t64_3.21.12-10%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./protobuf-compiler_3.21.12-10%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libpcre2-posix3_10.44-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libevent-2.1-7t64_2.1.12-stable-10%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libunbound8_1.22.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libblkid-dev_2.40.2-11_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libsepol2_3.7-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libsepol-dev_3.7-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libpcre2-16-0_10.44-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libpcre2-32-0_10.44-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libpcre2-dev_10.44-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libselinux1-dev_3.7-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libmount-dev_2.40.2-11_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libgirepository-2.0-0_2.82.2-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./girepository-tools_2.82.2-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libglib2.0-dev-bin_2.82.2-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libdw1t64_0.192-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libasm1t64_0.192-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libjson-c5_0.18%2bds-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libdebuginfod1t64_0.192-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./elfutils_0.192-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libbrotli-dev_1.1.0-2%2bb6_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libgnutls-dane0t64_3.8.8-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libgnutls-openssl27t64_3.8.8-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libidn2-dev_2.3.7-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libp11-kit-dev_0.25.5-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libtasn1-6-dev_4.19.0-3%2bb3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libgmpxx4ldbl_6.3.0%2bdfsg-2%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libgmp-dev_6.3.0%2bdfsg-2%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./nettle-dev_3.10-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libgnutls28-dev_3.8.8-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libgssrpc4t64_1.21.3-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libkadm5clnt-mit12_1.21.3-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libkdb5-10t64_1.21.3-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libkadm5srv-mit12_1.21.3-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./krb5-multidev_1.21.3-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libkrb5-dev_1.21.3-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libldap-dev_2.5.18%2bdfsg-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libpkgconf3_1.8.1-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./pkgconf-bin_1.8.1-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./pkgconf_1.8.1-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libnghttp2-dev_1.64.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libnghttp3-dev_1.4.0-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libngtcp2-crypto-gnutls-dev_1.6.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libngtcp2-dev_1.6.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libpsl-dev_0.21.2-1.1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./zlib1g-dev_1.3.dfsg%2breally1.3.1-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./librtmp-dev_2.4%2b20151223.gitfa8646d.1-2%2bb5_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libssl-dev_3.3.2-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libssh2-1-dev_1.11.1-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libzstd-dev_1.5.6%2bdfsg-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libcurl4-gnutls-dev_8.11.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libgcrypt20_1.11.0-6_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libxslt1.1_1.1.35-1.1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libyajl2_2.1.0-5%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libraptor2-0_2.0.16-4%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./icu-devtools_72.1-5%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libicu-dev_72.1-5%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libxml2-dev_2.12.7%2bdfsg%2breally2.9.14-0.2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libxslt1-dev_1.1.35-1.1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libyajl-dev_2.1.0-5%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libraptor2-dev_2.0.16-4%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./fastahack_1.0.0%2bdfsg-11%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libmhash2_0.9.9.9-10_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./librasqal3t64_0.9.33-2.1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./librasqal3-dev_0.9.33-2.1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libsimde-dev_0.8.2-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./xsltproc_1.1.35-1.1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libpng-dev_1.6.44-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libltdl7_2.4.7-8_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libelf-dev_0.192-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libdisorder-dev_0.0.2%2bgit20130809.8062ee1-4%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libsmithwaterman-dev_0.0%2bgit20160702.2610e25-12%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./raptor2-utils_2.0.16-4%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./python3-jaraco.context_6.0.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./librdf0t64_1.0.17-4%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./librdf0-dev_1.0.17-4%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libxau-dev_1.0.11-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libxdmcp-dev_1.1.5-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libxcb1-dev_1.17.0-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libxcb-shm0-dev_1.17.0-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libsysprof-capture-4-dev_47.1-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./help2man_1.49.3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./rs_20200313-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libffi-dev_3.4.6-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libgio-2.0-dev_2.82.2-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libglib2.0-data_2.82.2-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libglib2.0-bin_2.82.2-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libglib2.0-dev_2.82.2-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./tabix_1.20%2bds-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libbz2-dev_1.0.8-6_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libfreetype-dev_2.13.3%2bdfsg-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libwfa2-dev_2.3.3-4%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./pv_1.9.0-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./liblz4-dev_1.9.4-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./libosp5_1.5.2-15%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./opensp_1.5.2-15%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./docbook-to-man_2.0.0-47%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./docbook-xml_4.5-13_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./docbook-xsl_1.79.2%2bdfsg-7_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./python3-lxml_5.3.0-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./python3-autocommand_2.2.2-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./python3-more-itertools_10.5.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./python3-typing-extensions_4.12.2-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./python3-typeguard_4.4.1-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./python3-inflect_7.3.1-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./python3-jaraco.functools_4.1.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:12] "GET /./python3-pkg-resources_75.2.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./python3-pygments_2.18.0%2bdfsg-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./gtk-doc-tools_1.34.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libboost1.83-dev_1.83.0-3.2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libboost-program-options1.83.0_1.83.0-3.2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libboost-program-options1.83-dev_1.83.0-3.2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libboost-program-options-dev_1.83.0.2%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libprotobuf-lite32t64_3.21.12-10%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libprotobuf-dev_3.21.12-10%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libdivsufsort3_2.0.1-6%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libdivsufsort-dev_2.0.1-6%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./xtrans-dev_1.4.0-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libx11-dev_1.8.10-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libxext-dev_1.3.4-1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./liblzo2-2_2.10-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libcairo-script-interpreter2_1.18.2-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libexpat1-dev_2.6.4-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libfontconfig-dev_2.15.0-1.1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libpixman-1-dev_0.44.0-3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libsm-dev_1.2.4-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libxcb-render0-dev_1.17.0-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libxrender-dev_0.9.10-1.1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libcairo2-dev_1.18.2-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libdw-dev_0.192-4_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libncurses6_6.5-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libncurses-dev_6.5-2%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libdeflate-dev_1.22-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libhts-dev_1.20%2bds-2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libtabixpp-dev_1.1.2-2.1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./xxd_9.1.0861-1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./samtools_1.20-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libbackward-cpp-dev_1.6-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libtsl-hopscotch-map-dev_2.3.1-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libssw0_1.1-15%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libssw-dev_1.1-15%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libonig5_6.9.9-1%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./rapidjson-dev_1.1.0%2bdfsg2-7.3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libsparsehash-dev_2.0.3-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libprotoc-dev_3.21.12-10%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libjq1_1.7.1-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./jq_1.7.1-3%2bb1_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libfastahack-dev_1.0.0%2bdfsg-11%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libvcflib-dev_1.0.9%2bdfsg1-3%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./rasqal-utils_0.9.33-2.1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libjansson-dev_2.14-2%2bb3_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libfml0_0.1%2bgit20190320.b499514-1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./libfml-dev_0.1%2bgit20190320.b499514-1%2bb2_arm64.deb HTTP/1.1" 200 - 127.0.0.1 - - [27/Nov/2025 13:06:13] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmp7u9y51lc/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.dh5ete4z_g Reading package lists... Building dependency tree... Reading state information... libidn2-0 is already the newest version (2.3.7-2+b1). libidn2-0 set to manually installed. native-architecture is already the newest version (0.2.3). native-architecture set to manually installed. r-cran-littler is already the newest version (0.3.20-1+b1). r-cran-littler set to manually installed. ca-certificates is already the newest version (20240203). ca-certificates set to manually installed. liblzma-dev is already the newest version (5.6.3-1+b1). liblzma-dev set to manually installed. libvcflib-tools is already the newest version (1.0.9+dfsg1-3+b2). libvcflib-tools set to manually installed. libcairo-gobject2 is already the newest version (1.18.2-2). libcairo-gobject2 set to manually installed. libselinux1 is already the newest version (3.7-3+b1). uuid-dev is already the newest version (2.40.2-11). uuid-dev set to manually installed. docbook is already the newest version (4.5-11). docbook set to manually installed. libxss1 is already the newest version (1:1.2.3-1+b2). libxss1 set to manually installed. libgpg-error0 is already the newest version (1.50-4). libgpg-error0 set to manually installed. libjemalloc-dev is already the newest version (5.3.0-2+b2). libjemalloc-dev set to manually installed. libbz2-1.0 is already the newest version (1.0.8-6). libmd0 is already the newest version (1.1.0-2+b1). libxdmcp6 is already the newest version (1:1.1.5-1). libxdmcp6 set to manually installed. libelf1t64 is already the newest version (0.192-4). libelf1t64 set to manually installed. libgio-2.0-dev-bin is already the newest version (2.82.2-3). libgio-2.0-dev-bin set to manually installed. libice-dev is already the newest version (2:1.1.1-1). libice-dev set to manually installed. libcap-ng0 is already the newest version (0.8.5-3+b1). protobuf-compiler is already the newest version (3.21.12-10+b1). protobuf-compiler set to manually installed. libpam-runtime is already the newest version (1.5.3-7). tzdata is already the newest version (2024b-3). tzdata set to manually installed. libjpeg62-turbo is already the newest version (1:2.1.5-3+b1). libjpeg62-turbo set to manually installed. libaudit1 is already the newest version (1:4.0.2-2). sgml-data is already the newest version (2.0.11+nmu1). sgml-data set to manually installed. libdb5.3t64 is already the newest version (5.3.28+dfsg2-9). libdebuginfod-common is already the newest version (0.192-4). libdebuginfod-common set to manually installed. libpcre2-posix3 is already the newest version (10.44-4). libpcre2-posix3 set to manually installed. cmake is already the newest version (3.31.1-1). cmake set to manually installed. libunbound8 is already the newest version (1.22.0-1). libunbound8 set to manually installed. libp11-kit0 is already the newest version (0.25.5-2+b1). libp11-kit0 set to manually installed. bsdutils is already the newest version (1:2.40.2-11). liblsan0 is already the newest version (14.2.0-8). liblsan0 set to manually installed. debhelper is already the newest version (13.20). debhelper set to manually installed. libmount-dev is already the newest version (2.40.2-11). libmount-dev set to manually installed. po-debconf is already the newest version (1.0.21+nmu1). po-debconf set to manually installed. r-cran-scales is already the newest version (1.3.0-1). r-cran-scales set to manually installed. libglib2.0-dev-bin is already the newest version (2.82.2-3). libglib2.0-dev-bin set to manually installed. libstdc++-14-dev is already the newest version (14.2.0-8). libstdc++-14-dev set to manually installed. libreadline8t64 is already the newest version (8.2-5). libreadline8t64 set to manually installed. elfutils is already the newest version (0.192-4). elfutils set to manually installed. libraptor2-dev is already the newest version (2.0.16-4+b1). libraptor2-dev set to manually installed. r-cran-tibble is already the newest version (3.2.1+dfsg-2+b1). r-cran-tibble set to manually installed. fastahack is already the newest version (1.0.0+dfsg-11+b2). fastahack set to manually installed. libuv1t64 is already the newest version (1.48.0-7). libuv1t64 set to manually installed. unzip is already the newest version (6.0-28+b1). unzip set to manually installed. librasqal3-dev is already the newest version (0.9.33-2.1+b2). librasqal3-dev set to manually installed. libnghttp2-dev is already the newest version (1.64.0-1). libnghttp2-dev set to manually installed. libtasn1-6 is already the newest version (4.19.0-3+b3). libtasn1-6 set to manually installed. libsimde-dev is already the newest version (0.8.2-1). libsimde-dev set to manually installed. libxxhash0 is already the newest version (0.8.2-2+b2). libxxhash0 set to manually installed. xsltproc is already the newest version (1.1.35-1.1+b1). xsltproc set to manually installed. libgnutls30t64 is already the newest version (3.8.8-2). libgnutls30t64 set to manually installed. libgcc-s1 is already the newest version (14.2.0-8). libuchardet0 is already the newest version (0.0.8-1+b2). libuchardet0 set to manually installed. libmount1 is already the newest version (2.40.2-11). libpng-dev is already the newest version (1.6.44-2). libpng-dev set to manually installed. libdebhelper-perl is already the newest version (13.20). libdebhelper-perl set to manually installed. libjansson4 is already the newest version (2.14-2+b3). libjansson4 set to manually installed. libprotobuf32t64 is already the newest version (3.21.12-10+b1). libprotobuf32t64 set to manually installed. build-essential is already the newest version (12.12). build-essential set to manually installed. libsigsegv2 is already the newest version (2.14-1+b2). libsigsegv2 set to manually installed. libltdl7 is already the newest version (2.4.7-8). libltdl7 set to manually installed. libelf-dev is already the newest version (0.192-4). libelf-dev set to manually installed. libgnutls-dane0t64 is already the newest version (3.8.8-2). libgnutls-dane0t64 set to manually installed. libsmithwaterman-dev is already the newest version (0.0+git20160702.2610e25-12+b2). libsmithwaterman-dev set to manually installed. libmhash2 is already the newest version (0.9.9.9-10). libmhash2 set to manually installed. libpam0g is already the newest version (1.5.3-7+b1). libgcc-14-dev is already the newest version (14.2.0-8). libgcc-14-dev set to manually installed. libhogweed6t64 is already the newest version (3.10-1+b1). libhogweed6t64 set to manually installed. raptor2-utils is already the newest version (2.0.16-4+b1). raptor2-utils set to manually installed. libnghttp3-9 is already the newest version (1.4.0-1+b1). libnghttp3-9 set to manually installed. libsepol2 is already the newest version (3.7-1). libsepol2 set to manually installed. python3.12-minimal is already the newest version (3.12.7-3). python3.12-minimal set to manually installed. readline-common is already the newest version (8.2-5). readline-common set to manually installed. python3-jaraco.context is already the newest version (6.0.0-1). python3-jaraco.context set to manually installed. sensible-utils is already the newest version (0.0.24). sensible-utils set to manually installed. r-cran-magrittr is already the newest version (2.0.3-1+b1). r-cran-magrittr set to manually installed. bison is already the newest version (2:3.8.2+dfsg-1+b2). bison set to manually installed. r-cran-rlang is already the newest version (1.1.4-1+b1). r-cran-rlang set to manually installed. perl-base is already the newest version (5.40.0-7). make is already the newest version (4.3-4.1+b1). make set to manually installed. libxcb-render0 is already the newest version (1.17.0-2+b1). libxcb-render0 set to manually installed. librdf0-dev is already the newest version (1.0.17-4+b1). librdf0-dev set to manually installed. libxcb-shm0-dev is already the newest version (1.17.0-2+b1). libxcb-shm0-dev set to manually installed. findutils is already the newest version (4.10.0-3). libsysprof-capture-4-dev is already the newest version (47.1-1). libsysprof-capture-4-dev set to manually installed. libsasl2-2 is already the newest version (2.1.28+dfsg1-8). libsasl2-2 set to manually installed. librdf0t64 is already the newest version (1.0.17-4+b1). librdf0t64 set to manually installed. dpkg is already the newest version (1.22.11). help2man is already the newest version (1.49.3+b1). help2man set to manually installed. librtmp1 is already the newest version (2.4+20151223.gitfa8646d.1-2+b5). librtmp1 set to manually installed. x11proto-dev is already the newest version (2024.1-1). x11proto-dev set to manually installed. gcc-14-base is already the newest version (14.2.0-8). r-cran-glue is already the newest version (1.7.0-1+b1). r-cran-glue set to manually installed. rs is already the newest version (20200313-1+b1). rs set to manually installed. libuuid1 is already the newest version (2.40.2-11). pkgconf is already the newest version (1.8.1-4). pkgconf set to manually installed. libglib2.0-dev is already the newest version (2.82.2-3). libglib2.0-dev set to manually installed. libssh2-1t64 is already the newest version (1.11.1-1). libssh2-1t64 set to manually installed. openssl-provider-legacy is already the newest version (3.3.2-2). tabix is already the newest version (1.20+ds-2). tabix set to manually installed. libfreetype-dev is already the newest version (2.13.3+dfsg-1). libfreetype-dev set to manually installed. libwfa2-dev is already the newest version (2.3.3-4+b1). libwfa2-dev set to manually installed. python3.12 is already the newest version (3.12.7-3). python3.12 set to manually installed. r-cran-munsell is already the newest version (0.5.1-1). r-cran-munsell set to manually installed. flex is already the newest version (2.6.4-8.2+b3). flex set to manually installed. libpkgconf3 is already the newest version (1.8.1-4). libpkgconf3 set to manually installed. libsmithwaterman0 is already the newest version (0.0+git20160702.2610e25-12+b2). libsmithwaterman0 set to manually installed. libmpc3 is already the newest version (1.3.1-1+b3). libmpc3 set to manually installed. pv is already the newest version (1.9.0-1). pv set to manually installed. libglib2.0-data is already the newest version (2.82.2-3). libglib2.0-data set to manually installed. libthai-data is already the newest version (0.1.29-2). libthai-data set to manually installed. libsepol-dev is already the newest version (3.7-1). libsepol-dev set to manually installed. g++-14 is already the newest version (14.2.0-8). g++-14 set to manually installed. libselinux1-dev is already the newest version (3.7-3+b1). libselinux1-dev set to manually installed. gcc is already the newest version (4:14.2.0-1). gcc set to manually installed. libdpkg-perl is already the newest version (1.22.11). libdpkg-perl set to manually installed. libcurl4t64 is already the newest version (8.11.0-1). libcurl4t64 set to manually installed. dpkg-dev is already the newest version (1.22.11). dpkg-dev set to manually installed. libxcb1 is already the newest version (1.17.0-2+b1). libxcb1 set to manually installed. python3-minimal is already the newest version (3.12.7-1). python3-minimal set to manually installed. r-cran-pillar is already the newest version (1.9.0+dfsg-1). r-cran-pillar set to manually installed. liblz4-dev is already the newest version (1.9.4-3+b1). liblz4-dev set to manually installed. libpsl-dev is already the newest version (0.21.2-1.1+b1). libpsl-dev set to manually installed. dh-strip-nondeterminism is already the newest version (1.14.0-1). dh-strip-nondeterminism set to manually installed. gtk-doc-tools is already the newest version (1.34.0-1). gtk-doc-tools set to manually installed. libboost-program-options-dev is already the newest version (1.83.0.2+b2). libboost-program-options-dev set to manually installed. python3-more-itertools is already the newest version (10.5.0-1). python3-more-itertools set to manually installed. autotools-dev is already the newest version (20220109.1). autotools-dev set to manually installed. libldap-dev is already the newest version (2.5.18+dfsg-3+b1). libldap-dev set to manually installed. r-cran-rcpp is already the newest version (1.0.13-1-1). r-cran-rcpp set to manually installed. bc is already the newest version (1.07.1-4+b1). bc set to manually installed. xdg-utils is already the newest version (1.1.3-4.1). xdg-utils set to manually installed. libmagic-mgc is already the newest version (1:5.45-3+b1). libmagic-mgc set to manually installed. libpango-1.0-0 is already the newest version (1.54.0+ds-3). libpango-1.0-0 set to manually installed. python3 is already the newest version (3.12.7-1). python3 set to manually installed. python3-pygments is already the newest version (2.18.0+dfsg-1). python3-pygments set to manually installed. libngtcp2-dev is already the newest version (1.6.0-1). libngtcp2-dev set to manually installed. r-cran-r6 is already the newest version (2.5.1-1). r-cran-r6 set to manually installed. usr-is-merged is already the newest version (39). libtirpc3t64 is already the newest version (1.3.4+ds-1.3+b1). libtirpc3t64 set to manually installed. libgfortran5 is already the newest version (14.2.0-8). libgfortran5 set to manually installed. r-cran-gtable is already the newest version (0.3.6+dfsg-1). r-cran-gtable set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.1-1+b1). libxml2 is already the newest version (2.12.7+dfsg+really2.9.14-0.2+b1). libxml2 set to manually installed. hostname is already the newest version (3.25). r-cran-lattice is already the newest version (0.22-6-1+b1). r-cran-lattice set to manually installed. libnghttp3-dev is already the newest version (1.4.0-1+b1). libnghttp3-dev set to manually installed. python3-autocommand is already the newest version (2.2.2-3). python3-autocommand set to manually installed. libtk8.6 is already the newest version (8.6.15-1). libtk8.6 set to manually installed. r-cran-matrix is already the newest version (1.7-1-1). r-cran-matrix set to manually installed. libgdbm-compat4t64 is already the newest version (1.24-2). libgdbm-compat4t64 set to manually installed. libprotobuf-dev is already the newest version (3.21.12-10+b1). libprotobuf-dev set to manually installed. libncursesw6 is already the newest version (6.5-2+b1). libncursesw6 set to manually installed. cpp-14 is already the newest version (14.2.0-8). cpp-14 set to manually installed. libice6 is already the newest version (2:1.1.1-1). libice6 set to manually installed. libdivsufsort-dev is already the newest version (2.0.1-6+b1). libdivsufsort-dev set to manually installed. libxext-dev is already the newest version (2:1.3.4-1+b2). libxext-dev set to manually installed. libpam-modules is already the newest version (1.5.3-7+b1). libcrypt1 is already the newest version (1:4.4.36-5). libgmp10 is already the newest version (2:6.3.0+dfsg-2+b2). python3-lxml is already the newest version (5.3.0-1+b1). python3-lxml set to manually installed. libxft2 is already the newest version (2.3.6-1+b2). libxft2 set to manually installed. rpcsvc-proto is already the newest version (1.4.3-1+b1). rpcsvc-proto set to manually installed. r-cran-pkgkitten is already the newest version (0.2.4-1). r-cran-pkgkitten set to manually installed. r-cran-plyr is already the newest version (1.8.9-1+b1). r-cran-plyr set to manually installed. libitm1 is already the newest version (14.2.0-8). libitm1 set to manually installed. r-cran-cli is already the newest version (3.6.3-1). r-cran-cli set to manually installed. libpng16-16t64 is already the newest version (1.6.44-2). libpng16-16t64 set to manually installed. libblas3 is already the newest version (3.12.0-4). libblas3 set to manually installed. libc-dev-bin is already the newest version (2.40-3). libc-dev-bin set to manually installed. gettext-base is already the newest version (0.22.5-2). gettext-base set to manually installed. perl-modules-5.40 is already the newest version (5.40.0-7). perl-modules-5.40 set to manually installed. libpcre2-16-0 is already the newest version (10.44-4). libpcre2-16-0 set to manually installed. libdivsufsort3 is already the newest version (2.0.1-6+b1). libdivsufsort3 set to manually installed. libtiff6 is already the newest version (4.5.1+git230720-5). libtiff6 set to manually installed. cpp-14-aarch64-linux-gnu is already the newest version (14.2.0-8). cpp-14-aarch64-linux-gnu set to manually installed. libcairo-script-interpreter2 is already the newest version (1.18.2-2). libcairo-script-interpreter2 set to manually installed. gcc-14 is already the newest version (14.2.0-8). gcc-14 set to manually installed. libbrotli-dev is already the newest version (1.1.0-2+b6). libbrotli-dev set to manually installed. libgio-2.0-dev is already the newest version (2.82.2-3). libgio-2.0-dev set to manually installed. libcairo2-dev is already the newest version (1.18.2-2). libcairo2-dev set to manually installed. libprotoc32t64 is already the newest version (3.21.12-10+b1). libprotoc32t64 set to manually installed. libngtcp2-crypto-gnutls8 is already the newest version (1.6.0-1). libngtcp2-crypto-gnutls8 set to manually installed. libharfbuzz0b is already the newest version (10.0.1-1). libharfbuzz0b set to manually installed. libhts3t64 is already the newest version (1.20+ds-2). libhts3t64 set to manually installed. binutils is already the newest version (2.43.1-5). binutils set to manually installed. libdw-dev is already the newest version (0.192-4). libdw-dev set to manually installed. r-cran-mass is already the newest version (7.3-61-1+b1). r-cran-mass set to manually installed. cmake-data is already the newest version (3.31.1-1). cmake-data set to manually installed. libpaper1 is already the newest version (1.1.29+b2). libpaper1 set to manually installed. python3-typeguard is already the newest version (4.4.1-1). python3-typeguard set to manually installed. automake is already the newest version (1:1.16.5-1.3). automake set to manually installed. libldap-2.5-0 is already the newest version (2.5.18+dfsg-3+b1). libldap-2.5-0 set to manually installed. libsmartcols1 is already the newest version (2.40.2-11). file is already the newest version (1:5.45-3+b1). file set to manually installed. libgmpxx4ldbl is already the newest version (2:6.3.0+dfsg-2+b2). libgmpxx4ldbl set to manually installed. libboost1.83-dev is already the newest version (1.83.0-3.2+b1). libboost1.83-dev set to manually installed. libthai0 is already the newest version (0.1.29-2+b1). libthai0 set to manually installed. libcom-err2 is already the newest version (1.47.1-1+b1). libcom-err2 set to manually installed. libtasn1-6-dev is already the newest version (4.19.0-3+b3). libtasn1-6-dev set to manually installed. gzip is already the newest version (1.12-1.1+b1). libpcre2-32-0 is already the newest version (10.44-4). libpcre2-32-0 set to manually installed. python3-packaging is already the newest version (24.2-1). python3-packaging set to manually installed. xtrans-dev is already the newest version (1.4.0-1). xtrans-dev set to manually installed. libngtcp2-16 is already the newest version (1.6.0-1). libngtcp2-16 set to manually installed. libpsl5t64 is already the newest version (0.21.2-1.1+b1). libpsl5t64 set to manually installed. libncurses-dev is already the newest version (6.5-2+b1). libncurses-dev set to manually installed. libpython3.12-minimal is already the newest version (3.12.7-3). libpython3.12-minimal set to manually installed. libyajl2 is already the newest version (2.1.0-5+b2). libyajl2 set to manually installed. diffutils is already the newest version (1:3.10-1+b1). libdebconfclient0 is already the newest version (0.273). debianutils is already the newest version (5.21). libicu-dev is already the newest version (72.1-5+b1). libicu-dev set to manually installed. libasan8 is already the newest version (14.2.0-8). libasan8 set to manually installed. libtabixpp-dev is already the newest version (1.1.2-2.1+b1). libtabixpp-dev set to manually installed. xxd is already the newest version (2:9.1.0861-1). xxd set to manually installed. libnsl2 is already the newest version (1.3.0-3+b3). libnsl2 set to manually installed. fonts-dejavu-mono is already the newest version (2.37-8). fonts-dejavu-mono set to manually installed. m4 is already the newest version (1.4.19-4). m4 set to manually installed. libprotobuf-lite32t64 is already the newest version (3.21.12-10+b1). libprotobuf-lite32t64 set to manually installed. dh-autoreconf is already the newest version (20). dh-autoreconf set to manually installed. libgnutls28-dev is already the newest version (3.8.8-2). libgnutls28-dev set to manually installed. libngtcp2-crypto-gnutls-dev is already the newest version (1.6.0-1). libngtcp2-crypto-gnutls-dev set to manually installed. opensp is already the newest version (1.5.2-15+b1). opensp set to manually installed. librhash1 is already the newest version (1.4.5-1). librhash1 set to manually installed. binutils-aarch64-linux-gnu is already the newest version (2.43.1-5). binutils-aarch64-linux-gnu set to manually installed. docbook-xsl is already the newest version (1.79.2+dfsg-7). docbook-xsl set to manually installed. r-cran-vctrs is already the newest version (0.6.5-1+b1). r-cran-vctrs set to manually installed. dash is already the newest version (0.5.12-9+b1). libjsoncpp26 is already the newest version (1.9.6-3). libjsoncpp26 set to manually installed. libxau-dev is already the newest version (1:1.0.11-1). libxau-dev set to manually installed. xorg-sgml-doctools is already the newest version (1:1.11-1.1). xorg-sgml-doctools set to manually installed. libfontconfig-dev is already the newest version (2.15.0-1.1+b1). libfontconfig-dev set to manually installed. libbz2-dev is already the newest version (1.0.8-6). libbz2-dev set to manually installed. libperl5.40 is already the newest version (5.40.0-7). libperl5.40 set to manually installed. libhts-dev is already the newest version (1.20+ds-2). libhts-dev set to manually installed. libdisorder0 is already the newest version (0.0.2+git20130809.8062ee1-4+b2). libdisorder0 set to manually installed. libx11-6 is already the newest version (2:1.8.10-2). libx11-6 set to manually installed. libc-bin is already the newest version (2.40-3). cpp is already the newest version (4:14.2.0-1). cpp set to manually installed. bsdextrautils is already the newest version (2.40.2-11). bsdextrautils set to manually installed. liblzma5 is already the newest version (5.6.3-1+b1). libx11-dev is already the newest version (2:1.8.10-2). libx11-dev set to manually installed. python3-jaraco.functools is already the newest version (4.1.0-1). python3-jaraco.functools set to manually installed. netbase is already the newest version (6.4). netbase set to manually installed. libcap2 is already the newest version (1:2.66-5+b1). libctf-nobfd0 is already the newest version (2.43.1-5). libctf-nobfd0 set to manually installed. libosp5 is already the newest version (1.5.2-15+b1). libosp5 set to manually installed. libseccomp2 is already the newest version (2.5.5-1+b3). libseccomp2 set to manually installed. r-cran-viridislite is already the newest version (0.4.2-2). r-cran-viridislite set to manually installed. libzstd1 is already the newest version (1.5.6+dfsg-1+b1). libunistring5 is already the newest version (1.2-1+b1). libunistring5 set to manually installed. fontconfig-config is already the newest version (2.15.0-1.1+b1). fontconfig-config set to manually installed. patch is already the newest version (2.7.6-7+b1). patch set to manually installed. samtools is already the newest version (1.20-3+b1). samtools set to manually installed. libxt6t64 is already the newest version (1:1.2.1-1.2+b1). libxt6t64 set to manually installed. libbackward-cpp-dev is already the newest version (1.6-1). libbackward-cpp-dev set to manually installed. libcrypt-dev is already the newest version (1:4.4.36-5). libcrypt-dev set to manually installed. xz-utils is already the newest version (5.6.3-1+b1). xz-utils set to manually installed. r-cran-gridbase is already the newest version (0.4-7-5). r-cran-gridbase set to manually installed. r-cran-pkgconfig is already the newest version (2.0.3-2). r-cran-pkgconfig set to manually installed. libxslt1.1 is already the newest version (1.1.35-1.1+b1). libxslt1.1 set to manually installed. autoconf is already the newest version (2.72-3). autoconf set to manually installed. libpixman-1-0 is already the newest version (0.44.0-3). libpixman-1-0 set to manually installed. sed is already the newest version (4.9-2+b1). libdisorder-dev is already the newest version (0.0.2+git20130809.8062ee1-4+b2). libdisorder-dev set to manually installed. libffi8 is already the newest version (3.4.6-1). libffi8 set to manually installed. libkdb5-10t64 is already the newest version (1.21.3-3). libkdb5-10t64 set to manually installed. libhtscodecs2 is already the newest version (1.6.1-1). libhtscodecs2 set to manually installed. libnettle8t64 is already the newest version (3.10-1+b1). libnettle8t64 set to manually installed. util-linux is already the newest version (2.40.2-11). autopoint is already the newest version (0.22.5-2). autopoint set to manually installed. libkrb5-3 is already the newest version (1.21.3-3). libkrb5-3 set to manually installed. libsm6 is already the newest version (2:1.2.4-1). libsm6 set to manually installed. libhwasan0 is already the newest version (14.2.0-8). libhwasan0 set to manually installed. x11-common is already the newest version (1:7.7+23.1). x11-common set to manually installed. fonts-dejavu-core is already the newest version (2.37-8). fonts-dejavu-core set to manually installed. libboost-program-options1.83.0 is already the newest version (1.83.0-3.2+b1). libboost-program-options1.83.0 set to manually installed. r-cran-utf8 is already the newest version (1.2.4-1+b1). r-cran-utf8 set to manually installed. libwfa2-0 is already the newest version (2.3.3-4+b1). libwfa2-0 set to manually installed. libxau6 is already the newest version (1:1.0.11-1). libxau6 set to manually installed. libgmp-dev is already the newest version (2:6.3.0+dfsg-2+b2). libgmp-dev set to manually installed. libssh2-1-dev is already the newest version (1.11.1-1). libssh2-1-dev set to manually installed. libpcre2-8-0 is already the newest version (10.44-4). libubsan1 is already the newest version (14.2.0-8). libubsan1 set to manually installed. libpcre2-dev is already the newest version (10.44-4). libpcre2-dev set to manually installed. libaudit-common is already the newest version (1:4.0.2-2). python3-pkg-resources is already the newest version (75.2.0-1). python3-pkg-resources set to manually installed. fontconfig is already the newest version (2.15.0-1.1+b1). fontconfig set to manually installed. libxrender1 is already the newest version (1:0.9.10-1.1+b2). libxrender1 set to manually installed. dwz is already the newest version (0.15-1+b1). dwz set to manually installed. libattr1 is already the newest version (1:2.5.2-2). libsasl2-modules-db is already the newest version (2.1.28+dfsg1-8). libsasl2-modules-db set to manually installed. libmpfr6 is already the newest version (4.2.1-1+b2). libmpfr6 set to manually installed. sysvinit-utils is already the newest version (3.11-1). libfile-stripnondeterminism-perl is already the newest version (1.14.0-1). libfile-stripnondeterminism-perl set to manually installed. openssl is already the newest version (3.3.2-2). openssl set to manually installed. libxext6 is already the newest version (2:1.3.4-1+b2). libxext6 set to manually installed. libcurl4-gnutls-dev is already the newest version (8.11.0-1). libcurl4-gnutls-dev set to manually installed. docbook-xml is already the newest version (4.5-13). docbook-xml set to manually installed. libidn2-dev is already the newest version (2.3.7-2+b1). libidn2-dev set to manually installed. libssl3t64 is already the newest version (3.3.2-2). binutils-common is already the newest version (2.43.1-5). binutils-common set to manually installed. libzstd-dev is already the newest version (1.5.6+dfsg-1+b1). libzstd-dev set to manually installed. libjbig0 is already the newest version (2.1-6.1+b2). libjbig0 set to manually installed. groff-base is already the newest version (1.23.0-5). groff-base set to manually installed. r-base-core is already the newest version (4.4.2-1). r-base-core set to manually installed. liblapack3 is already the newest version (3.12.0-4). liblapack3 set to manually installed. r-cran-fansi is already the newest version (1.0.5-1+b1). r-cran-fansi set to manually installed. libxrender-dev is already the newest version (1:0.9.10-1.1+b2). libxrender-dev set to manually installed. libxdmcp-dev is already the newest version (1:1.1.5-1). libxdmcp-dev set to manually installed. libsharpyuv0 is already the newest version (1.4.0-0.1+b1). libsharpyuv0 set to manually installed. libcurl3t64-gnutls is already the newest version (8.11.0-1). libcurl3t64-gnutls set to manually installed. libkadm5srv-mit12 is already the newest version (1.21.3-3). libkadm5srv-mit12 set to manually installed. libnghttp2-14 is already the newest version (1.64.0-1). libnghttp2-14 set to manually installed. libjson-c5 is already the newest version (0.18+ds-1). libjson-c5 set to manually installed. libatomic1 is already the newest version (14.2.0-8). libatomic1 set to manually installed. libpangocairo-1.0-0 is already the newest version (1.54.0+ds-3). libpangocairo-1.0-0 set to manually installed. libglib2.0-0t64 is already the newest version (2.82.2-3). libglib2.0-0t64 set to manually installed. linux-libc-dev is already the newest version (6.11.9-1). linux-libc-dev set to manually installed. libproc2-0 is already the newest version (2:4.0.4-6). libproc2-0 set to manually installed. r-cran-nlme is already the newest version (3.1.166-1). r-cran-nlme set to manually installed. libpaper-utils is already the newest version (1.1.29+b2). libpaper-utils set to manually installed. libtsl-hopscotch-map-dev is already the newest version (2.3.1-1). libtsl-hopscotch-map-dev set to manually installed. procps is already the newest version (2:4.0.4-6). procps set to manually installed. libdebuginfod1t64 is already the newest version (0.192-4). libdebuginfod1t64 set to manually installed. libk5crypto3 is already the newest version (1.21.3-3). libk5crypto3 set to manually installed. libtsan2 is already the newest version (14.2.0-8). libtsan2 set to manually installed. libssw-dev is already the newest version (1.1-15+b1). libssw-dev set to manually installed. libxml2-dev is already the newest version (2.12.7+dfsg+really2.9.14-0.2+b1). libxml2-dev set to manually installed. r-cran-labeling is already the newest version (0.4.3-1). r-cran-labeling set to manually installed. bzip2 is already the newest version (1.0.8-6). bzip2 set to manually installed. g++-14-aarch64-linux-gnu is already the newest version (14.2.0-8). g++-14-aarch64-linux-gnu set to manually installed. r-cran-withr is already the newest version (3.0.2+dfsg-1). r-cran-withr set to manually installed. init-system-helpers is already the newest version (1.67). libgnutls-openssl27t64 is already the newest version (3.8.8-2). libgnutls-openssl27t64 set to manually installed. libonig5 is already the newest version (6.9.9-1+b1). libonig5 set to manually installed. libpython3.12-stdlib is already the newest version (3.12.7-3). libpython3.12-stdlib set to manually installed. base-passwd is already the newest version (3.6.5). libstdc++6 is already the newest version (14.2.0-8). libstdc++6 set to manually installed. libxcb1-dev is already the newest version (1.17.0-2+b1). libxcb1-dev set to manually installed. libxcb-render0-dev is already the newest version (1.17.0-2+b1). libxcb-render0-dev set to manually installed. libctf0 is already the newest version (2.43.1-5). libctf0 set to manually installed. libarchive13t64 is already the newest version (3.7.4-1.1). libarchive13t64 set to manually installed. gcc-aarch64-linux-gnu is already the newest version (4:14.2.0-1). gcc-aarch64-linux-gnu set to manually installed. liblzo2-2 is already the newest version (2.10-3+b1). liblzo2-2 set to manually installed. libexpat1-dev is already the newest version (2.6.4-1). libexpat1-dev set to manually installed. libraptor2-0 is already the newest version (2.0.16-4+b1). libraptor2-0 set to manually installed. libtcl8.6 is already the newest version (8.6.15+dfsg-2). libtcl8.6 set to manually installed. gettext is already the newest version (0.22.5-2). gettext set to manually installed. liblz4-1 is already the newest version (1.9.4-3+b1). liblz4-1 set to manually installed. docbook-to-man is already the newest version (1:2.0.0-47+b1). docbook-to-man set to manually installed. comerr-dev is already the newest version (2.1-1.47.1-1+b1). comerr-dev set to manually installed. libtool is already the newest version (2.4.7-8). libtool set to manually installed. libgomp1 is already the newest version (14.2.0-8). libgomp1 set to manually installed. python3-inflect is already the newest version (7.3.1-2). python3-inflect set to manually installed. cpp-aarch64-linux-gnu is already the newest version (4:14.2.0-1). cpp-aarch64-linux-gnu set to manually installed. mawk is already the newest version (1.3.4.20240905-1). libdeflate0 is already the newest version (1.22-1). libdeflate0 set to manually installed. rapidjson-dev is already the newest version (1.1.0+dfsg2-7.3). rapidjson-dev set to manually installed. libdatrie1 is already the newest version (0.2.13-3+b1). libdatrie1 set to manually installed. libgssrpc4t64 is already the newest version (1.21.3-3). libgssrpc4t64 set to manually installed. libdw1t64 is already the newest version (0.192-4). libdw1t64 set to manually installed. libsm-dev is already the newest version (2:1.2.4-1). libsm-dev set to manually installed. libcc1-0 is already the newest version (14.2.0-8). libcc1-0 set to manually installed. r-cran-colorspace is already the newest version (2.1-1+dfsg-1). r-cran-colorspace set to manually installed. libsparsehash-dev is already the newest version (2.0.3-2). libsparsehash-dev set to manually installed. libprotoc-dev is already the newest version (3.21.12-10+b1). libprotoc-dev set to manually installed. libtirpc-common is already the newest version (1.3.4+ds-1.3). libtirpc-common set to manually installed. ncurses-base is already the newest version (6.5-2). gawk is already the newest version (1:5.2.1-2+b2). gawk set to manually installed. libpipeline1 is already the newest version (1.5.8-1). libpipeline1 set to manually installed. libgcrypt20 is already the newest version (1.11.0-6). libgcrypt20 set to manually installed. libncurses6 is already the newest version (6.5-2+b1). libncurses6 set to manually installed. bwa is already the newest version (0.7.18-1). bwa set to manually installed. jq is already the newest version (1.7.1-3+b1). jq set to manually installed. libsystemd0 is already the newest version (257~rc2-3). ncurses-bin is already the newest version (6.5-2+b1). libffi-dev is already the newest version (3.4.6-1). libffi-dev set to manually installed. libbrotli1 is already the newest version (1.1.0-2+b6). libbrotli1 set to manually installed. r-cran-farver is already the newest version (2.1.2-1+b1). r-cran-farver set to manually installed. libfontconfig1 is already the newest version (2.15.0-1.1+b1). libfontconfig1 set to manually installed. media-types is already the newest version (10.1.0). media-types set to manually installed. libvcflib-dev is already the newest version (1.0.9+dfsg1-3+b2). libvcflib-dev set to manually installed. libkadm5clnt-mit12 is already the newest version (1.21.3-3). libkadm5clnt-mit12 set to manually installed. libtabixpp0t64 is already the newest version (1.1.2-2.1+b1). libtabixpp0t64 set to manually installed. libwebp7 is already the newest version (1.4.0-0.1+b1). libwebp7 set to manually installed. libfastahack0 is already the newest version (1.0.0+dfsg-11+b2). libfastahack0 set to manually installed. zip is already the newest version (3.0-14+b1). zip set to manually installed. libc6-dev is already the newest version (2.40-3). libc6-dev set to manually installed. libjq1 is already the newest version (1.7.1-3+b1). libjq1 set to manually installed. debconf is already the newest version (1.5.87). coreutils is already the newest version (9.5-1+b1). libpangoft2-1.0-0 is already the newest version (1.54.0+ds-3). libpangoft2-1.0-0 set to manually installed. libgssapi-krb5-2 is already the newest version (1.21.3-3). libgssapi-krb5-2 set to manually installed. g++ is already the newest version (4:14.2.0-1). g++ set to manually installed. libp11-kit-dev is already the newest version (0.25.5-2+b1). libp11-kit-dev set to manually installed. r-cran-ggplot2 is already the newest version (3.5.1+dfsg-1). r-cran-ggplot2 set to manually installed. libpython3-stdlib is already the newest version (3.12.7-1). libpython3-stdlib set to manually installed. rasqal-utils is already the newest version (0.9.33-2.1+b2). rasqal-utils set to manually installed. libc6 is already the newest version (2.40-3). libgraphite2-3 is already the newest version (1.3.14-2+b1). libgraphite2-3 set to manually installed. libkeyutils1 is already the newest version (1.6.3-4). libkeyutils1 set to manually installed. libacl1 is already the newest version (2.3.2-2+b1). ucf is already the newest version (3.0043+nmu1). ucf set to manually installed. intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. libssw0 is already the newest version (1.1-15+b1). libssw0 set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libexpat1 is already the newest version (2.6.4-1). libexpat1 set to manually installed. r-cran-lifecycle is already the newest version (1.0.4+dfsg-1). r-cran-lifecycle set to manually installed. librtmp-dev is already the newest version (2.4+20151223.gitfa8646d.1-2+b5). librtmp-dev set to manually installed. libgdbm6t64 is already the newest version (1.24-2). libgdbm6t64 set to manually installed. base-files is already the newest version (13.5). libvcflib2 is already the newest version (1.0.9+dfsg1-3+b2). libvcflib2 set to manually installed. libsqlite3-0 is already the newest version (3.46.1-1). libsqlite3-0 set to manually installed. libjansson-dev is already the newest version (2.14-2+b3). libjansson-dev set to manually installed. libkrb5-dev is already the newest version (1.21.3-3). libkrb5-dev set to manually installed. libmagic1t64 is already the newest version (1:5.45-3+b1). libmagic1t64 set to manually installed. libkrb5support0 is already the newest version (1.21.3-3). libkrb5support0 set to manually installed. libjemalloc2 is already the newest version (5.3.0-2+b2). libjemalloc2 set to manually installed. krb5-multidev is already the newest version (1.21.3-3). krb5-multidev set to manually installed. libx11-data is already the newest version (2:1.8.10-2). libx11-data set to manually installed. libblkid-dev is already the newest version (2.40.2-11). libblkid-dev set to manually installed. libpixman-1-dev is already the newest version (0.44.0-3). libpixman-1-dev set to manually installed. libsframe1 is already the newest version (2.43.1-5). libsframe1 set to manually installed. libasm1t64 is already the newest version (0.192-4). libasm1t64 set to manually installed. libssl-dev is already the newest version (3.3.2-2). libssl-dev set to manually installed. pkgconf-bin is already the newest version (1.8.1-4). pkgconf-bin set to manually installed. python3-typing-extensions is already the newest version (4.12.2-2). python3-typing-extensions set to manually installed. xml-core is already the newest version (0.19). xml-core set to manually installed. g++-aarch64-linux-gnu is already the newest version (4:14.2.0-1). g++-aarch64-linux-gnu set to manually installed. nettle-dev is already the newest version (3.10-1+b1). nettle-dev set to manually installed. libfreetype6 is already the newest version (2.13.3+dfsg-1). libfreetype6 set to manually installed. icu-devtools is already the newest version (72.1-5+b1). icu-devtools set to manually installed. libudev1 is already the newest version (257~rc2-3). libboost-program-options1.83-dev is already the newest version (1.83.0-3.2+b1). libboost-program-options1.83-dev set to manually installed. girepository-tools is already the newest version (2.82.2-3). girepository-tools set to manually installed. r-cran-rcolorbrewer is already the newest version (1.1-3-1). r-cran-rcolorbrewer set to manually installed. libfribidi0 is already the newest version (1.0.15-1). libfribidi0 set to manually installed. libglib2.0-bin is already the newest version (2.82.2-3). libglib2.0-bin set to manually installed. libgirepository-2.0-0 is already the newest version (2.82.2-3). libgirepository-2.0-0 set to manually installed. liblocale-gettext-perl is already the newest version (1.07-7+b1). liblocale-gettext-perl set to manually installed. libblkid1 is already the newest version (2.40.2-11). librasqal3t64 is already the newest version (0.9.33-2.1+b2). librasqal3t64 set to manually installed. libbinutils is already the newest version (2.43.1-5). libbinutils set to manually installed. libxcb-shm0 is already the newest version (1.17.0-2+b1). libxcb-shm0 set to manually installed. libicu72 is already the newest version (72.1-5+b1). libicu72 set to manually installed. zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.1-1+b1). zlib1g-dev set to manually installed. libfml-dev is already the newest version (0.1+git20190320.b499514-1+b2). libfml-dev set to manually installed. r-cran-mgcv is already the newest version (1.9-1-1+b1). r-cran-mgcv set to manually installed. perl is already the newest version (5.40.0-7). perl set to manually installed. littler is already the newest version (0.3.20-1). littler set to manually installed. libyajl-dev is already the newest version (2.1.0-5+b2). libyajl-dev set to manually installed. bash is already the newest version (5.2.32-1+b2). man-db is already the newest version (2.13.0-1). man-db set to manually installed. grep is already the newest version (3.11-4+b1). libpam-modules-bin is already the newest version (1.5.3-7+b1). libisl23 is already the newest version (0.27-1). libisl23 set to manually installed. libcairo2 is already the newest version (1.18.2-2). libcairo2 set to manually installed. liblerc4 is already the newest version (4.0.0+ds-5). liblerc4 set to manually installed. tar is already the newest version (1.35+dfsg-3+b1). libtinfo6 is already the newest version (6.5-2+b1). libfml0 is already the newest version (0.1+git20190320.b499514-1+b2). libfml0 set to manually installed. sgml-base is already the newest version (1.31). sgml-base set to manually installed. libfastahack-dev is already the newest version (1.0.0+dfsg-11+b2). libfastahack-dev set to manually installed. libdeflate-dev is already the newest version (1.22-1). libdeflate-dev set to manually installed. libevent-2.1-7t64 is already the newest version (2.1.12-stable-10+b1). libevent-2.1-7t64 set to manually installed. libgprofng0 is already the newest version (2.43.1-5). libgprofng0 set to manually installed. libxslt1-dev is already the newest version (1.1.35-1.1+b1). libxslt1-dev set to manually installed. r-cran-isoband is already the newest version (0.2.7-1+b1). r-cran-isoband set to manually installed. gcc-14-aarch64-linux-gnu is already the newest version (14.2.0-8). gcc-14-aarch64-linux-gnu set to manually installed. The following NEW packages will be installed: x11proto-core-dev 127.0.0.1 - - [27/Nov/2025 13:07:28] "GET /./x11proto-core-dev_2024.1-1_all.deb HTTP/1.1" 200 - 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 3312 B of archives. After this operation, 11.3 kB of additional disk space will be used. Get:1 http://localhost:43463 ./ x11proto-core-dev 2024.1-1 [3312 B] Fetched 3312 B in 0s (171 kB/s) Chrooting into /srv/rebuilderd/tmp/mmdebstrap.dh5ete4z_g/ Selecting previously unselected package x11proto-core-dev. (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 ... 52106 files and directories currently installed.) Preparing to unpack .../x11proto-core-dev_2024.1-1_all.deb ... Unpacking x11proto-core-dev (2024.1-1) ... Chrooting into /srv/rebuilderd/tmp/mmdebstrap.dh5ete4z_g/ Setting up x11proto-core-dev (2024.1-1) ... I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg -r debootsnap-dummy' exec /srv/rebuilderd/tmp/mmdebstrap.dh5ete4z_g (Reading database ... 52109 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.dh5ete4z_g I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.dh5ete4z_g I: running special hook: upload sources.list /etc/apt/sources.list I: waiting for background processes to finish... I: PID 9109 exited with exit code 0 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.dh5ete4z_g... I: success in 97.9583 seconds Downloading dependency 386 of 475: media-types:arm64=10.1.0 Downloading dependency 387 of 475: libvcflib-dev:arm64=1.0.9+dfsg1-3+b2 Downloading dependency 388 of 475: libkadm5clnt-mit12:arm64=1.21.3-3 Downloading dependency 389 of 475: libtabixpp0t64:arm64=1.1.2-2.1+b1 Downloading dependency 390 of 475: libwebp7:arm64=1.4.0-0.1+b1 Downloading dependency 391 of 475: libfastahack0:arm64=1.0.0+dfsg-11+b2 Downloading dependency 392 of 475: zip:arm64=3.0-14+b1 Downloading dependency 393 of 475: libc6-dev:arm64=2.40-3 Downloading dependency 394 of 475: libjq1:arm64=1.7.1-3+b1 Downloading dependency 395 of 475: debconf:arm64=1.5.87 Downloading dependency 396 of 475: coreutils:arm64=9.5-1+b1 Downloading dependency 397 of 475: libpangoft2-1.0-0:arm64=1.54.0+ds-3 Downloading dependency 398 of 475: libgssapi-krb5-2:arm64=1.21.3-3 Downloading dependency 399 of 475: g++:arm64=4:14.2.0-1 Downloading dependency 400 of 475: libp11-kit-dev:arm64=0.25.5-2+b1 Downloading dependency 401 of 475: r-cran-ggplot2:arm64=3.5.1+dfsg-1 Downloading dependency 402 of 475: libpython3-stdlib:arm64=3.12.7-1 Downloading dependency 403 of 475: rasqal-utils:arm64=0.9.33-2.1+b2 Downloading dependency 404 of 475: libc6:arm64=2.40-3 Downloading dependency 405 of 475: libgraphite2-3:arm64=1.3.14-2+b1 Downloading dependency 406 of 475: libkeyutils1:arm64=1.6.3-4 Downloading dependency 407 of 475: libacl1:arm64=2.3.2-2+b1 Downloading dependency 408 of 475: ucf:arm64=3.0043+nmu1 Downloading dependency 409 of 475: intltool-debian:arm64=0.35.0+20060710.6 Downloading dependency 410 of 475: libssw0:arm64=1.1-15+b1 Downloading dependency 411 of 475: libarchive-zip-perl:arm64=1.68-1 Downloading dependency 412 of 475: libexpat1:arm64=2.6.4-1 Downloading dependency 413 of 475: r-cran-lifecycle:arm64=1.0.4+dfsg-1 Downloading dependency 414 of 475: librtmp-dev:arm64=2.4+20151223.gitfa8646d.1-2+b5 Downloading dependency 415 of 475: libgdbm6t64:arm64=1.24-2 Downloading dependency 416 of 475: base-files:arm64=13.5 Downloading dependency 417 of 475: libvcflib2:arm64=1.0.9+dfsg1-3+b2 Downloading dependency 418 of 475: libsqlite3-0:arm64=3.46.1-1 Downloading dependency 419 of 475: libjansson-dev:arm64=2.14-2+b3 Downloading dependency 420 of 475: libkrb5-dev:arm64=1.21.3-3 Downloading dependency 421 of 475: libmagic1t64:arm64=1:5.45-3+b1 Downloading dependency 422 of 475: libkrb5support0:arm64=1.21.3-3 Downloading dependency 423 of 475: libjemalloc2:arm64=5.3.0-2+b2 Downloading dependency 424 of 475: krb5-multidev:arm64=1.21.3-3 Downloading dependency 425 of 475: libx11-data:arm64=2:1.8.10-2 Downloading dependency 426 of 475: libblkid-dev:arm64=2.40.2-11 Downloading dependency 427 of 475: libpixman-1-dev:arm64=0.44.0-3 Downloading dependency 428 of 475: libsframe1:arm64=2.43.1-5 Downloading dependency 429 of 475: libasm1t64:arm64=0.192-4 Downloading dependency 430 of 475: libssl-dev:arm64=3.3.2-2 Downloading dependency 431 of 475: pkgconf-bin:arm64=1.8.1-4 Downloading dependency 432 of 475: python3-typing-extensions:arm64=4.12.2-2 Downloading dependency 433 of 475: xml-core:arm64=0.19 Downloading dependency 434 of 475: g++-aarch64-linux-gnu:arm64=4:14.2.0-1 Downloading dependency 435 of 475: nettle-dev:arm64=3.10-1+b1 Downloading dependency 436 of 475: libfreetype6:arm64=2.13.3+dfsg-1 Downloading dependency 437 of 475: icu-devtools:arm64=72.1-5+b1 Downloading dependency 438 of 475: libudev1:arm64=257~rc2-3 Downloading dependency 439 of 475: libboost-program-options1.83-dev:arm64=1.83.0-3.2+b1 Downloading dependency 440 of 475: girepository-tools:arm64=2.82.2-3 Downloading dependency 441 of 475: r-cran-rcolorbrewer:arm64=1.1-3-1 Downloading dependency 442 of 475: libfribidi0:arm64=1.0.15-1 Downloading dependency 443 of 475: libglib2.0-bin:arm64=2.82.2-3 Downloading dependency 444 of 475: libgirepository-2.0-0:arm64=2.82.2-3 Downloading dependency 445 of 475: liblocale-gettext-perl:arm64=1.07-7+b1 Downloading dependency 446 of 475: libblkid1:arm64=2.40.2-11 Downloading dependency 447 of 475: librasqal3t64:arm64=0.9.33-2.1+b2 Downloading dependency 448 of 475: libbinutils:arm64=2.43.1-5 Downloading dependency 449 of 475: libxcb-shm0:arm64=1.17.0-2+b1 Downloading dependency 450 of 475: libicu72:arm64=72.1-5+b1 Downloading dependency 451 of 475: zlib1g-dev:arm64=1:1.3.dfsg+really1.3.1-1+b1 Downloading dependency 452 of 475: libfml-dev:arm64=0.1+git20190320.b499514-1+b2 Downloading dependency 453 of 475: r-cran-mgcv:arm64=1.9-1-1+b1 Downloading dependency 454 of 475: perl:arm64=5.40.0-7 Downloading dependency 455 of 475: littler:arm64=0.3.20-1 Downloading dependency 456 of 475: libyajl-dev:arm64=2.1.0-5+b2 Downloading dependency 457 of 475: bash:arm64=5.2.32-1+b2 Downloading dependency 458 of 475: man-db:arm64=2.13.0-1 Downloading dependency 459 of 475: grep:arm64=3.11-4+b1 Downloading dependency 460 of 475: x11proto-core-dev:arm64=2024.1-1 Downloading dependency 461 of 475: libpam-modules-bin:arm64=1.5.3-7+b1 Downloading dependency 462 of 475: libisl23:arm64=0.27-1 Downloading dependency 463 of 475: libcairo2:arm64=1.18.2-2 Downloading dependency 464 of 475: liblerc4:arm64=4.0.0+ds-5 Downloading dependency 465 of 475: tar:arm64=1.35+dfsg-3+b1 Downloading dependency 466 of 475: libtinfo6:arm64=6.5-2+b1 Downloading dependency 467 of 475: libfml0:arm64=0.1+git20190320.b499514-1+b2 Downloading dependency 468 of 475: sgml-base:arm64=1.31 Downloading dependency 469 of 475: libfastahack-dev:arm64=1.0.0+dfsg-11+b2 Downloading dependency 470 of 475: libdeflate-dev:arm64=1.22-1 Downloading dependency 471 of 475: libevent-2.1-7t64:arm64=2.1.12-stable-10+b1 Downloading dependency 472 of 475: libgprofng0:arm64=2.43.1-5 Downloading dependency 473 of 475: libxslt1-dev:arm64=1.1.35-1.1+b1 Downloading dependency 474 of 475: r-cran-isoband:arm64=0.2.7-1+b1 Downloading dependency 475 of 475: gcc-14-aarch64-linux-gnu:arm64=14.2.0-8 env --chdir=/srv/rebuilderd/tmp/rebuilderd6UeE2X/out DEB_BUILD_OPTIONS=parallel=4 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1732147972 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildrpcfaR/debrebuild.sbuildrc.2blrC8fPZ7pK sbuild --build=arm64 --host=arm64 --no-source --arch-any --no-arch-all --chroot=/srv/rebuilderd/tmp/debrebuildrpcfaR/debrebuild.tar.3ffhIjAJfD1i --chroot-mode=unshare --dist=unstable --no-run-lintian --no-run-piuparts --no-run-autopkgtest --no-apt-update --no-apt-upgrade --no-apt-distupgrade --starting-build-commands=grep -iq "^Rules-Requires-Root:" "%p/debian/control" || sed -i "1iRules-Requires-Root: no" "%p/debian/control" --verbose --nolog --bd-uninstallable-explainer= --build-path=/build/reproducible-path --dsc-dir=vg-1.59.0+ds /srv/rebuilderd/tmp/rebuilderd6UeE2X/inputs/vg_1.59.0+ds-0.1.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+deb13u1 (16 August 2025) on codethink02-arm64 +==============================================================================+ | vg 1.59.0+ds-0.1 (arm64) Thu, 27 Nov 2025 13:07:37 +0000 | +==============================================================================+ Package: vg Version: 1.59.0+ds-0.1 Source Version: 1.59.0+ds-0.1 Distribution: unstable Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/rebuilderd/tmp/debrebuildrpcfaR/debrebuild.tar.3ffhIjAJfD1i to /srv/rebuilderd/tmp/tmp.sbuild.va7noC76q5... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Thu, 27 Nov 2025 13:07:46 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderd6UeE2X/inputs/vg_1.59.0+ds-0.1.dsc exists in /srv/rebuilderd/tmp/rebuilderd6UeE2X/inputs; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Thu, 27 Nov 2025 13:07:48 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), pv, bsdextrautils | bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa, protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libtinfo6, libncurses-dev, automake, libtool, jq, samtools, unzip, librdf0-dev, cmake, pkgconf, bc, gtk-doc-tools, raptor2-utils, rasqal-utils, bison, flex, gawk, liblz4-dev, liblzma-dev, libcairo2-dev, libpixman-1-dev, libdeflate-dev, libboost-program-options-dev, libjemalloc-dev, libbackward-cpp-dev, elfutils, libdw-dev, libelf-dev, libraptor2-dev, libsparsehash-dev, rapidjson-dev, libfml-dev, libfastahack-dev, fastahack, tabix, xxd, libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools, libhts-dev, help2man, python3:any, libsimde-dev, libzstd-dev, build-essential Filtered Build-Depends: debhelper-compat (= 13), pv, bsdextrautils, zlib1g-dev, rs, libffi-dev, bwa, protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libtinfo6, libncurses-dev, automake, libtool, jq, samtools, unzip, librdf0-dev, cmake, pkgconf, bc, gtk-doc-tools, raptor2-utils, rasqal-utils, bison, flex, gawk, liblz4-dev, liblzma-dev, libcairo2-dev, libpixman-1-dev, libdeflate-dev, libboost-program-options-dev, libjemalloc-dev, libbackward-cpp-dev, elfutils, libdw-dev, libelf-dev, libraptor2-dev, libsparsehash-dev, rapidjson-dev, libfml-dev, libfastahack-dev, fastahack, tabix, xxd, libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools, libhts-dev, help2man, python3:any, libsimde-dev, libzstd-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-F7MfER/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Thu, 27 Nov 2025 13:07:54 +0000 | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in amd64 arm64 ppc64el mips64el s390x riscv64 x32 all) +------------------------------------------------------------------------------+ | Build environment Thu, 27 Nov 2025 13:07:55 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.57+deb13-cloud-arm64 #1 SMP Debian 6.12.57-1 (2025-11-05) arm64 (aarch64) Toolchain package versions: binutils_2.43.1-5 dpkg-dev_1.22.11 g++-14_14.2.0-8 gcc-14_14.2.0-8 libc6-dev_2.40-3 libstdc++-14-dev_14.2.0-8 libstdc++6_14.2.0-8 linux-libc-dev_6.11.9-1 Package versions: autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.5 bash_5.2.32-1+b2 bc_1.07.1-4+b1 binutils_2.43.1-5 binutils-aarch64-linux-gnu_2.43.1-5 binutils-common_2.43.1-5 bison_2:3.8.2+dfsg-1+b2 bsdextrautils_2.40.2-11 bsdutils_1:2.40.2-11 build-essential_12.12 bwa_0.7.18-1 bzip2_1.0.8-6 ca-certificates_20240203 cmake_3.31.1-1 cmake-data_3.31.1-1 comerr-dev_2.1-1.47.1-1+b1 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-14_14.2.0-8 cpp-14-aarch64-linux-gnu_14.2.0-8 cpp-aarch64-linux-gnu_4:14.2.0-1 dash_0.5.12-9+b1 debconf_1.5.87 debhelper_13.20 debianutils_5.21 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1+b1 docbook_4.5-11 docbook-to-man_1:2.0.0-47+b1 docbook-xml_4.5-13 docbook-xsl_1.79.2+dfsg-7 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 elfutils_0.192-4 fastahack_1.0.0+dfsg-11+b2 file_1:5.45-3+b1 findutils_4.10.0-3 flex_2.6.4-8.2+b3 fontconfig_2.15.0-1.1+b1 fontconfig-config_2.15.0-1.1+b1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 g++_4:14.2.0-1 g++-14_14.2.0-8 g++-14-aarch64-linux-gnu_14.2.0-8 g++-aarch64-linux-gnu_4:14.2.0-1 gawk_1:5.2.1-2+b2 gcc_4:14.2.0-1 gcc-14_14.2.0-8 gcc-14-aarch64-linux-gnu_14.2.0-8 gcc-14-base_14.2.0-8 gcc-aarch64-linux-gnu_4:14.2.0-1 gettext_0.22.5-2 gettext-base_0.22.5-2 girepository-tools_2.82.2-3 grep_3.11-4+b1 groff-base_1.23.0-5 gtk-doc-tools_1.34.0-1 gzip_1.12-1.1+b1 help2man_1.49.3+b1 hostname_3.25 icu-devtools_72.1-5+b1 init-system-helpers_1.67 intltool-debian_0.35.0+20060710.6 jq_1.7.1-3+b1 krb5-multidev_1.21.3-3 libacl1_2.3.2-2+b1 libarchive-zip-perl_1.68-1 libarchive13t64_3.7.4-1.1 libasan8_14.2.0-8 libasm1t64_0.192-4 libatomic1_14.2.0-8 libattr1_1:2.5.2-2 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2 libbackward-cpp-dev_1.6-1 libbinutils_2.43.1-5 libblas3_3.12.0-4 libblkid-dev_2.40.2-11 libblkid1_2.40.2-11 libboost-program-options-dev_1.83.0.2+b2 libboost-program-options1.83-dev_1.83.0-3.2+b1 libboost-program-options1.83.0_1.83.0-3.2+b1 libboost1.83-dev_1.83.0-3.2+b1 libbrotli-dev_1.1.0-2+b6 libbrotli1_1.1.0-2+b6 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.40-3 libc-dev-bin_2.40-3 libc6_2.40-3 libc6-dev_2.40-3 libcairo-gobject2_1.18.2-2 libcairo-script-interpreter2_1.18.2-2 libcairo2_1.18.2-2 libcairo2-dev_1.18.2-2 libcap-ng0_0.8.5-3+b1 libcap2_1:2.66-5+b1 libcc1-0_14.2.0-8 libcom-err2_1.47.1-1+b1 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-5 libctf0_2.43.1-5 libcurl3t64-gnutls_8.11.0-1 libcurl4-gnutls-dev_8.11.0-1 libcurl4t64_8.11.0-1 libdatrie1_0.2.13-3+b1 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.273 libdebhelper-perl_13.20 libdebuginfod-common_0.192-4 libdebuginfod1t64_0.192-4 libdeflate-dev_1.22-1 libdeflate0_1.22-1 libdisorder-dev_0.0.2+git20130809.8062ee1-4+b2 libdisorder0_0.0.2+git20130809.8062ee1-4+b2 libdivsufsort-dev_2.0.1-6+b1 libdivsufsort3_2.0.1-6+b1 libdpkg-perl_1.22.11 libdw-dev_0.192-4 libdw1t64_0.192-4 libelf-dev_0.192-4 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libexpat1_2.6.4-1 libexpat1-dev_2.6.4-1 libfastahack-dev_1.0.0+dfsg-11+b2 libfastahack0_1.0.0+dfsg-11+b2 libffi-dev_3.4.6-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libfml-dev_0.1+git20190320.b499514-1+b2 libfml0_0.1+git20190320.b499514-1+b2 libfontconfig-dev_2.15.0-1.1+b1 libfontconfig1_2.15.0-1.1+b1 libfreetype-dev_2.13.3+dfsg-1 libfreetype6_2.13.3+dfsg-1 libfribidi0_1.0.15-1 libgcc-14-dev_14.2.0-8 libgcc-s1_14.2.0-8 libgcrypt20_1.11.0-6 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgfortran5_14.2.0-8 libgio-2.0-dev_2.82.2-3 libgio-2.0-dev-bin_2.82.2-3 libgirepository-2.0-0_2.82.2-3 libglib2.0-0t64_2.82.2-3 libglib2.0-bin_2.82.2-3 libglib2.0-data_2.82.2-3 libglib2.0-dev_2.82.2-3 libglib2.0-dev-bin_2.82.2-3 libgmp-dev_2:6.3.0+dfsg-2+b2 libgmp10_2:6.3.0+dfsg-2+b2 libgmpxx4ldbl_2:6.3.0+dfsg-2+b2 libgnutls-dane0t64_3.8.8-2 libgnutls-openssl27t64_3.8.8-2 libgnutls28-dev_3.8.8-2 libgnutls30t64_3.8.8-2 libgomp1_14.2.0-8 libgpg-error0_1.50-4 libgprofng0_2.43.1-5 libgraphite2-3_1.3.14-2+b1 libgssapi-krb5-2_1.21.3-3 libgssrpc4t64_1.21.3-3 libharfbuzz0b_10.0.1-1 libhogweed6t64_3.10-1+b1 libhts-dev_1.20+ds-2 libhts3t64_1.20+ds-2 libhtscodecs2_1.6.1-1 libhwasan0_14.2.0-8 libice-dev_2:1.1.1-1 libice6_2:1.1.1-1 libicu-dev_72.1-5+b1 libicu72_72.1-5+b1 libidn2-0_2.3.7-2+b1 libidn2-dev_2.3.7-2+b1 libisl23_0.27-1 libitm1_14.2.0-8 libjansson-dev_2.14-2+b3 libjansson4_2.14-2+b3 libjbig0_2.1-6.1+b2 libjemalloc-dev_5.3.0-2+b2 libjemalloc2_5.3.0-2+b2 libjpeg62-turbo_1:2.1.5-3+b1 libjq1_1.7.1-3+b1 libjson-c5_0.18+ds-1 libjsoncpp26_1.9.6-3 libk5crypto3_1.21.3-3 libkadm5clnt-mit12_1.21.3-3 libkadm5srv-mit12_1.21.3-3 libkdb5-10t64_1.21.3-3 libkeyutils1_1.6.3-4 libkrb5-3_1.21.3-3 libkrb5-dev_1.21.3-3 libkrb5support0_1.21.3-3 liblapack3_3.12.0-4 libldap-2.5-0_2.5.18+dfsg-3+b1 libldap-dev_2.5.18+dfsg-3+b1 liblerc4_4.0.0+ds-5 liblocale-gettext-perl_1.07-7+b1 liblsan0_14.2.0-8 libltdl7_2.4.7-8 liblz4-1_1.9.4-3+b1 liblz4-dev_1.9.4-3+b1 liblzma-dev_5.6.3-1+b1 liblzma5_5.6.3-1+b1 liblzo2-2_2.10-3+b1 libmagic-mgc_1:5.45-3+b1 libmagic1t64_1:5.45-3+b1 libmd0_1.1.0-2+b1 libmhash2_0.9.9.9-10 libmount-dev_2.40.2-11 libmount1_2.40.2-11 libmpc3_1.3.1-1+b3 libmpfr6_4.2.1-1+b2 libncurses-dev_6.5-2+b1 libncurses6_6.5-2+b1 libncursesw6_6.5-2+b1 libnettle8t64_3.10-1+b1 libnghttp2-14_1.64.0-1 libnghttp2-dev_1.64.0-1 libnghttp3-9_1.4.0-1+b1 libnghttp3-dev_1.4.0-1+b1 libngtcp2-16_1.6.0-1 libngtcp2-crypto-gnutls-dev_1.6.0-1 libngtcp2-crypto-gnutls8_1.6.0-1 libngtcp2-dev_1.6.0-1 libnsl2_1.3.0-3+b3 libonig5_6.9.9-1+b1 libosp5_1.5.2-15+b1 libp11-kit-dev_0.25.5-2+b1 libp11-kit0_0.25.5-2+b1 libpam-modules_1.5.3-7+b1 libpam-modules-bin_1.5.3-7+b1 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7+b1 libpango-1.0-0_1.54.0+ds-3 libpangocairo-1.0-0_1.54.0+ds-3 libpangoft2-1.0-0_1.54.0+ds-3 libpaper-utils_1.1.29+b2 libpaper1_1.1.29+b2 libpcre2-16-0_10.44-4 libpcre2-32-0_10.44-4 libpcre2-8-0_10.44-4 libpcre2-dev_10.44-4 libpcre2-posix3_10.44-4 libperl5.40_5.40.0-7 libpipeline1_1.5.8-1 libpixman-1-0_0.44.0-3 libpixman-1-dev_0.44.0-3 libpkgconf3_1.8.1-4 libpng-dev_1.6.44-2 libpng16-16t64_1.6.44-2 libproc2-0_2:4.0.4-6 libprotobuf-dev_3.21.12-10+b1 libprotobuf-lite32t64_3.21.12-10+b1 libprotobuf32t64_3.21.12-10+b1 libprotoc-dev_3.21.12-10+b1 libprotoc32t64_3.21.12-10+b1 libpsl-dev_0.21.2-1.1+b1 libpsl5t64_0.21.2-1.1+b1 libpython3-stdlib_3.12.7-1 libpython3.12-minimal_3.12.7-3 libpython3.12-stdlib_3.12.7-3 libraptor2-0_2.0.16-4+b1 libraptor2-dev_2.0.16-4+b1 librasqal3-dev_0.9.33-2.1+b2 librasqal3t64_0.9.33-2.1+b2 librdf0-dev_1.0.17-4+b1 librdf0t64_1.0.17-4+b1 libreadline8t64_8.2-5 librhash1_1.4.5-1 librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5 librtmp1_2.4+20151223.gitfa8646d.1-2+b5 libsasl2-2_2.1.28+dfsg1-8 libsasl2-modules-db_2.1.28+dfsg1-8 libseccomp2_2.5.5-1+b3 libselinux1_3.7-3+b1 libselinux1-dev_3.7-3+b1 libsepol-dev_3.7-1 libsepol2_3.7-1 libsframe1_2.43.1-5 libsharpyuv0_1.4.0-0.1+b1 libsigsegv2_2.14-1+b2 libsimde-dev_0.8.2-1 libsm-dev_2:1.2.4-1 libsm6_2:1.2.4-1 libsmartcols1_2.40.2-11 libsmithwaterman-dev_0.0+git20160702.2610e25-12+b2 libsmithwaterman0_0.0+git20160702.2610e25-12+b2 libsparsehash-dev_2.0.3-2 libsqlite3-0_3.46.1-1 libssh2-1-dev_1.11.1-1 libssh2-1t64_1.11.1-1 libssl-dev_3.3.2-2 libssl3t64_3.3.2-2 libssw-dev_1.1-15+b1 libssw0_1.1-15+b1 libstdc++-14-dev_14.2.0-8 libstdc++6_14.2.0-8 libsysprof-capture-4-dev_47.1-1 libsystemd0_257~rc2-3 libtabixpp-dev_1.1.2-2.1+b1 libtabixpp0t64_1.1.2-2.1+b1 libtasn1-6_4.19.0-3+b3 libtasn1-6-dev_4.19.0-3+b3 libtcl8.6_8.6.15+dfsg-2 libthai-data_0.1.29-2 libthai0_0.1.29-2+b1 libtiff6_4.5.1+git230720-5 libtinfo6_6.5-2+b1 libtirpc-common_1.3.4+ds-1.3 libtirpc3t64_1.3.4+ds-1.3+b1 libtk8.6_8.6.15-1 libtool_2.4.7-8 libtsan2_14.2.0-8 libtsl-hopscotch-map-dev_2.3.1-1 libubsan1_14.2.0-8 libuchardet0_0.0.8-1+b2 libudev1_257~rc2-3 libunbound8_1.22.0-1 libunistring5_1.2-1+b1 libuuid1_2.40.2-11 libuv1t64_1.48.0-7 libvcflib-dev_1.0.9+dfsg1-3+b2 libvcflib-tools_1.0.9+dfsg1-3+b2 libvcflib2_1.0.9+dfsg1-3+b2 libwebp7_1.4.0-0.1+b1 libwfa2-0_2.3.3-4+b1 libwfa2-dev_2.3.3-4+b1 libx11-6_2:1.8.10-2 libx11-data_2:1.8.10-2 libx11-dev_2:1.8.10-2 libxau-dev_1:1.0.11-1 libxau6_1:1.0.11-1 libxcb-render0_1.17.0-2+b1 libxcb-render0-dev_1.17.0-2+b1 libxcb-shm0_1.17.0-2+b1 libxcb-shm0-dev_1.17.0-2+b1 libxcb1_1.17.0-2+b1 libxcb1-dev_1.17.0-2+b1 libxdmcp-dev_1:1.1.5-1 libxdmcp6_1:1.1.5-1 libxext-dev_2:1.3.4-1+b2 libxext6_2:1.3.4-1+b2 libxft2_2.3.6-1+b2 libxml2_2.12.7+dfsg+really2.9.14-0.2+b1 libxml2-dev_2.12.7+dfsg+really2.9.14-0.2+b1 libxrender-dev_1:0.9.10-1.1+b2 libxrender1_1:0.9.10-1.1+b2 libxslt1-dev_1.1.35-1.1+b1 libxslt1.1_1.1.35-1.1+b1 libxss1_1:1.2.3-1+b2 libxt6t64_1:1.2.1-1.2+b1 libxxhash0_0.8.2-2+b2 libyajl-dev_2.1.0-5+b2 libyajl2_2.1.0-5+b2 libzstd-dev_1.5.6+dfsg-1+b1 libzstd1_1.5.6+dfsg-1+b1 linux-libc-dev_6.11.9-1 littler_0.3.20-1 m4_1.4.19-4 make_4.3-4.1+b1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 media-types_10.1.0 native-architecture_0.2.3 ncurses-base_6.5-2 ncurses-bin_6.5-2+b1 netbase_6.4 nettle-dev_3.10-1+b1 opensp_1.5.2-15+b1 openssl_3.3.2-2 openssl-provider-legacy_3.3.2-2 patch_2.7.6-7+b1 perl_5.40.0-7 perl-base_5.40.0-7 perl-modules-5.40_5.40.0-7 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 procps_2:4.0.4-6 protobuf-compiler_3.21.12-10+b1 pv_1.9.0-1 python3_3.12.7-1 python3-autocommand_2.2.2-3 python3-inflect_7.3.1-2 python3-jaraco.context_6.0.0-1 python3-jaraco.functools_4.1.0-1 python3-lxml_5.3.0-1+b1 python3-minimal_3.12.7-1 python3-more-itertools_10.5.0-1 python3-packaging_24.2-1 python3-pkg-resources_75.2.0-1 python3-pygments_2.18.0+dfsg-1 python3-typeguard_4.4.1-1 python3-typing-extensions_4.12.2-2 python3.12_3.12.7-3 python3.12-minimal_3.12.7-3 r-base-core_4.4.2-1 r-cran-cli_3.6.3-1 r-cran-colorspace_2.1-1+dfsg-1 r-cran-fansi_1.0.5-1+b1 r-cran-farver_2.1.2-1+b1 r-cran-ggplot2_3.5.1+dfsg-1 r-cran-glue_1.7.0-1+b1 r-cran-gridbase_0.4-7-5 r-cran-gtable_0.3.6+dfsg-1 r-cran-isoband_0.2.7-1+b1 r-cran-labeling_0.4.3-1 r-cran-lattice_0.22-6-1+b1 r-cran-lifecycle_1.0.4+dfsg-1 r-cran-littler_0.3.20-1+b1 r-cran-magrittr_2.0.3-1+b1 r-cran-mass_7.3-61-1+b1 r-cran-matrix_1.7-1-1 r-cran-mgcv_1.9-1-1+b1 r-cran-munsell_0.5.1-1 r-cran-nlme_3.1.166-1 r-cran-pillar_1.9.0+dfsg-1 r-cran-pkgconfig_2.0.3-2 r-cran-pkgkitten_0.2.4-1 r-cran-plyr_1.8.9-1+b1 r-cran-r6_2.5.1-1 r-cran-rcolorbrewer_1.1-3-1 r-cran-rcpp_1.0.13-1-1 r-cran-rlang_1.1.4-1+b1 r-cran-scales_1.3.0-1 r-cran-tibble_3.2.1+dfsg-2+b1 r-cran-utf8_1.2.4-1+b1 r-cran-vctrs_0.6.5-1+b1 r-cran-viridislite_0.4.2-2 r-cran-withr_3.0.2+dfsg-1 rapidjson-dev_1.1.0+dfsg2-7.3 raptor2-utils_2.0.16-4+b1 rasqal-utils_0.9.33-2.1+b2 readline-common_8.2-5 rpcsvc-proto_1.4.3-1+b1 rs_20200313-1+b1 samtools_1.20-3+b1 sed_4.9-2+b1 sensible-utils_0.0.24 sgml-base_1.31 sgml-data_2.0.11+nmu1 sysvinit-utils_3.11-1 tabix_1.20+ds-2 tar_1.35+dfsg-3+b1 tzdata_2024b-3 ucf_3.0043+nmu1 unzip_6.0-28+b1 usr-is-merged_39 util-linux_2.40.2-11 uuid-dev_2.40.2-11 x11-common_1:7.7+23.1 x11proto-core-dev_2024.1-1 x11proto-dev_2024.1-1 xdg-utils_1.1.3-4.1 xml-core_0.19 xorg-sgml-doctools_1:1.11-1.1 xsltproc_1.1.35-1.1+b1 xtrans-dev_1.4.0-1 xxd_2:9.1.0861-1 xz-utils_5.6.3-1+b1 zip_3.0-14+b1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Thu, 27 Nov 2025 13:07:55 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: vg Binary: vg, vg-docs Architecture: amd64 arm64 ppc64el mips64el s390x riscv64 x32 all Version: 1.59.0+ds-0.1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: https://github.com/vgteam/vg#vg Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/vg Vcs-Git: https://salsa.debian.org/med-team/vg.git Testsuite: autopkgtest Testsuite-Triggers: libvcflib-tools Build-Depends: debhelper-compat (= 13), pv , bsdextrautils | bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa , protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libtinfo6, libncurses-dev, automake, libtool, jq, samtools , unzip, librdf0-dev, cmake, pkgconf, bc, gtk-doc-tools, raptor2-utils , rasqal-utils , bison, flex, gawk, liblz4-dev, liblzma-dev, libcairo2-dev, libpixman-1-dev, libdeflate-dev, libboost-program-options-dev, libjemalloc-dev, libbackward-cpp-dev, elfutils, libdw-dev, libelf-dev, libraptor2-dev, libsparsehash-dev, rapidjson-dev, libfml-dev, libfastahack-dev, fastahack , tabix , xxd , libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools , libhts-dev, help2man , python3:any, libsimde-dev, libzstd-dev Build-Depends-Indep: doxygen , graphviz Package-List: vg deb science optional arch=amd64,arm64,ppc64el,mips64el,s390x,riscv64,x32 vg-docs deb doc optional arch=all Checksums-Sha1: 9cceebb48fb18c8618654723085c6aaa4321f386 69705744 vg_1.59.0+ds.orig.tar.xz ddd7d9f6b17fee1f35ac6d3a00de3d7b2e6e491c 117112 vg_1.59.0+ds-0.1.debian.tar.xz Checksums-Sha256: 17e43b91bce35905caf9af98e3b839eeff296af7105c1df818eb81004e6ab144 69705744 vg_1.59.0+ds.orig.tar.xz dfd2b9a5f833d45b9b5632b651de59668380352bc87fa2654b2c2c7acf6c423b 117112 vg_1.59.0+ds-0.1.debian.tar.xz Files: e8aff1b3feff38a4085bf4fbee107ac9 69705744 vg_1.59.0+ds.orig.tar.xz 66279467d1d25d09cdba16f34999a366 117112 vg_1.59.0+ds-0.1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQHEBAEBCgAuFiEEQGIgyLhVKAI3jM5BH1x6i0VWQxQFAmc/WKIQHGJhZ2VAZGVi aWFuLm9yZwAKCRAfXHqLRVZDFHNzDAChrlW8GHppGU1D++m3+LBMHm1tEC4x4pa4 85La0aNeKtBpMqH6R7GpLZJ2HkdjXCqWdKXv60UYX7ughXFl30EQoAT8OM6+gN1w XUfB4XXa/OAvF0grSmIE08PL4nnvGcJlnXd5vW+DF/R8Ll7bIJLtWIn2kHV28uTk 9Faz9DRF4xEtNkVhHBcmlwxott+Zhf2Prt6XyjhUHegCRAd3aAcVrZQl87cR+gIj JpVjf1H9jBG4HhgZ7yxjDQmaosSgAuKf41GAyAl8YbxeLTcIfg3KYQ+LOWMDiRWv bucCUzqPlanDR5OtNk1+ORER59FE83oXSq1tLUMAeP53sE9jhVLFafwjWc5YqsRz XHkA0FGcYdlbcYUkRaXBKPHyvcBXrE81cA4CO9Afa8C3kgDwArYfq5OY08CE++/u 3t9vc+kT+wE9w3x6W81ywxyPchFlTEhjnoAZJ2kUhlVgsGNTT+9wi5Cbq9HFW6Lt 17nlcUFy3vPmaFg8qzO9Kte7eCqp1Q0= =YEjD -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./vg_1.59.0+ds-0.1.dsc: unsupported subcommand dpkg-source: info: extracting vg in /build/reproducible-path/vg-1.59.0+ds dpkg-source: info: unpacking vg_1.59.0+ds.orig.tar.xz dpkg-source: info: unpacking vg_1.59.0+ds-0.1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying avoid_abs_confusion dpkg-source: info: applying gcc-12 dpkg-source: info: applying use_packaged_libdeflate dpkg-source: info: applying use_packaged_jemalloc dpkg-source: info: applying use_packaged_libbackward-cpp dpkg-source: info: applying use_packaged_elfutils dpkg-source: info: applying use_packaged_raptor2 dpkg-source: info: applying no_need_for_snappy dpkg-source: info: applying use_packaged_sparsehash dpkg-source: info: applying use_packaged_fermi-lite dpkg-source: info: applying no_rpath dpkg-source: info: applying no_pg dpkg-source: info: applying use_packaged_fastahack dpkg-source: info: applying hardening_flags dpkg-source: info: applying static dpkg-source: info: applying use_packaged_lz4 dpkg-source: info: applying parallize_better dpkg-source: info: applying use_packaged_libtsl-hopscotch-map-dev dpkg-source: info: applying libVCFH_unneeded dpkg-source: info: applying better_clean dpkg-source: info: applying use_packaged_vcflib dpkg-source: info: applying use_packaged_htslib dpkg-source: info: applying simde dpkg-source: info: applying crossbuild dpkg-source: info: applying python3 Install fakeroot ---------------- Setup apt archive ----------------- Merged Build-Depends: fakeroot Filtered Build-Depends: fakeroot dpkg-deb: building package 'sbuild-build-depends-fakeroot-dummy' in '/build/reproducible-path/resolver-F7MfER/apt_archive/sbuild-build-depends-fakeroot-dummy.deb'. Install fakeroot build dependencies (apt-based resolver) -------------------------------------------------------- Installing build dependencies Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Thu, 27 Nov 2025 13:08:05 +0000 | +------------------------------------------------------------------------------+ grep -iq "^Rules-Requires-Root:" "/build/reproducible-path/vg-1.59.0+ds/debian/control" || sed -i "1iRules-Requires-Root: no" "/build/reproducible-path/vg-1.59.0+ds/debian/control" ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ I: Finished running 'grep -iq "^Rules-Requires-Root:" "/build/reproducible-path/vg-1.59.0+ds/debian/control" || sed -i "1iRules-Requires-Root: no" "/build/reproducible-path/vg-1.59.0+ds/debian/control"'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 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=1732147972 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -B dpkg-buildpackage: info: source package vg dpkg-buildpackage: info: source version 1.59.0+ds-0.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Bastian Germann dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' find /build/reproducible-path/vg-1.59.0+ds/include/ -type f -a '!' -name vg_git_version.hpp -delete dh_auto_clean || true make -j4 clean make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now rm -f -r bin/unittest rm -f -r lib rm -f -r obj/unittest/support rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/pic/io rm -f -r obj/io rm -f -r obj/pic/algorithms rm -f -r obj/algorithms rm -f -r obj/config rm -f -r obj/pic rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd C && make clean cd externalTools && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make clean cd quicktree_1.1 && make clean rm -rf ../bin ../lib make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' Makefile:2: ../sdsl-lite/Make.helper: No such file or directory make[3]: *** No rule to make target '../sdsl-lite/Make.helper'. Stop. make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' make[2]: *** [Makefile:854: clean] Error 2 make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_clean: error: make -j4 clean returned exit code 2 make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' rm -Rf ./deps/DYNAMIC/build/CMakeFiles dh_clean make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' dh_autoreconf --sourcedirectory=/build/reproducible-path/vg-1.59.0+ds/deps/vowpal_wabbit make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_auto_configure -a debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' mkdir -p /build/reproducible-path/vg-1.59.0+ds/debian/help find . -type d -name simde | xargs rm -Rf dh_auto_build -- all test/build_graph bin/shuf make -j4 "INSTALL=install --strip-program=true" all test/build_graph bin/shuf make[2]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' OS is Linux Compiler g++ is assumed to be GCC CXXFLAGS are -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp LDFLAGS are -Wl,-z,relro -Wl,-z,now . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" ./install.sh /build/reproducible-path/vg-1.59.0+ds . ./source_me.sh && cd deps/ssw/src && make && ar rs /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a ssw.o ssw_cpp.o && cp ssw_cpp.h ssw.h /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && cd deps/libhandlegraph && rm -Rf build CMakeCache.txt CMakeFiles && mkdir build && cd build && CXXFLAGS="-std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make && make install . ./source_me.sh && cd deps/kff-cpp-api && rm -Rf build && mkdir build && cd build && cmake .. && make && cp kff_io.hpp /build/reproducible-path/vg-1.59.0+ds/include && mv libkff.a /build/reproducible-path/vg-1.59.0+ds/lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' gcc -c -o ssw.o ssw.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. Library will be installed in '/build/reproducible-path/vg-1.59.0+ds' WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. CMake Deprecation Warning at CMakeLists.txt:1 (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. -- The C compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- The C compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting CXX compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting C compiler ABI info - done -- Detecting CXX compile features - done -- Configuring done (1.0s) -- Generating done (0.0s) -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build -- Detecting CXX compile features -- Detecting CXX compile features - done make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features libhandlegraph is root project or external_project -- Detecting C compile features - done -- Configuring done (1.0s) -- Compiler is recent enough to support C++14. -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks [ 16%] Building CXX object CMakeFiles/kff.dir/kff_io.cpp.o make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 2%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp -- Performing Test HAVE_GCC_STD=C__14__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS g++ -c -o ssw_cpp.o ssw_cpp.cpp -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success [ 5%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dfs.cpp -- Performing Test HAVE_CXA_DEMANGLE -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:102 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio gcc -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -fPIC -shared -o libssw.so ssw.c -- Looking for C++ include cstdio - found -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done (2.8s) In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [24, 248] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 8 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [25, 249] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 9 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [26, 250] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 10 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [27, 251] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 11 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [28, 252] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 12 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [29, 253] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 13 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [30, 254] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 14 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [24, 248] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 8 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [25, 249] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 9 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [26, 250] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 10 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [27, 251] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 11 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [28, 252] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 12 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [29, 253] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 13 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1167:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [30, 254] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 14 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [24, 248] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 8 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [25, 249] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 9 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [26, 250] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 10 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [27, 251] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 11 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [28, 252] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 12 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [29, 253] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 13 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1170:18: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘void Section_Minimizer::write_compacted_sequence_without_mini(uint8_t*, uint64_t, uint64_t, uint8_t*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset [30, 254] into destination object ‘buff’ of size 8 1164 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1164:17: note: at offset 14 into destination object ‘buff’ of size 8 [ 8%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/handle_graph.cpp -- Generating done (0.2s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 8 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bits.cpp.o -MF CMakeFiles/sdsl.dir/bits.cpp.o.d -o CMakeFiles/sdsl.dir/bits.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bits.cpp [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -MF CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o.d -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp [ 11%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [24, 248] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 8 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [25, 249] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 9 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [26, 250] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 10 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [27, 251] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 11 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [28, 252] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 12 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [29, 253] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 13 into destination object ‘buff’ of size 8 In function ‘void store_big_endian(uint8_t*, size_t, const T&) [with T = long unsigned int]’, inlined from ‘void Section_Raw::write_compacted_sequence(uint8_t*, uint64_t, uint8_t*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:950:18, inlined from ‘virtual void Section_Raw::copy(Kff_file*)’ at /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:1016:30: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:21:25: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 21 | *buff++ = data >> (8 * b); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp: In member function ‘virtual void Section_Raw::copy(Kff_file*)’: /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset [30, 254] into destination object ‘buff’ of size 8 947 | uint8_t buff[8]; | ^~~~ /build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/kff_io.cpp:947:17: note: at offset 14 into destination object ‘buff’ of size 8 gcc -o ssw_test ssw.o main.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -lm -lz [ 14%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_metadata.cpp [ 33%] Linking CXX static library libkff.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 33%] Built target kff make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' gcc -o example_c ssw.o example.c -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -lm -lz make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 50%] Building CXX object CMakeFiles/kff_example.dir/main.cpp.o g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -pipe -O3 -I. -lm -lz cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1358:27, inlined from ‘void sdsl::int_vector< >::resize(size_type) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:380:23, inlined from ‘sdsl::int_vector< >::int_vector(size_type, value_type, uint8_t) [with unsigned char t_width = 0]’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1285:11, inlined from ‘sdsl::excess::impl::impl()’ at /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:448:9: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 448 | *word &= | ^~~~~ make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/ssw/src' ar: creating /build/reproducible-path/vg-1.59.0+ds/lib/libssw.a . ./source_me.sh && cd deps/gssw && make && cp lib/libgssw.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp src/gssw.h /build/reproducible-path/vg-1.59.0+ds/include/ make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c src/gssw.c: In function ‘gssw_graph_print’: src/gssw.c:1947:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1947 | fprintf(stdout, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c:1951:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1951:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1951 | fprintf(stdout, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_stderr’: src/gssw.c:1963:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1963 | fprintf(stderr, "GRAPH // node %llu %u %s\n", n->id, n->len, n->seq); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c:1967:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c:1967:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1967 | fprintf(stderr, "GRAPH \"%llu %s\" -> \"%llu %s\";\n", n->prev[k]->id, n->prev[k]->seq, n->id, n->seq); | ~~~^ ~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu src/gssw.c: In function ‘gssw_graph_print_score_matrices’: src/gssw.c:1978:31: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 1978 | fprintf(out, "node %llu\n", n->id); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_print_graph_cigar’: src/gssw.c:3623:26: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 3623 | fprintf(out, "%llu[", nc->node->id); | ~~~^ ~~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_create_seed_byte’: src/gssw.c:5095:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5095 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu src/gssw.c: In function ‘gssw_create_seed_word’: src/gssw.c:5130:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 5130 | fprintf(stderr, "failing is node %llu\n", prev[k]->id); | ~~~^ ~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu [ 66%] Linking CXX executable kff_example make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 66%] Built target kff_example make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' [ 83%] Building CXX object benchmarks/CMakeFiles/reader_bench.dir/reader.cpp.o [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp [100%] Linking CXX executable reader_bench make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' src/gssw.c: In function ‘gssw_sw_software_byte’: src/gssw.c:277:5: warning: ‘__builtin_memcpy’ writing between 18446744071562067984 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 277 | memcpy(scratch, to_unswizzle, size); | ^ In function ‘unswizzle_byte’, inlined from ‘gssw_sw_software_byte’ at src/gssw.c:405:9: src/gssw.c:271:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 271 | uint8_t* scratch = (uint8_t*) malloc(size * sizeof(uint8_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [100%] Built target reader_bench make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/kff-cpp-api/build' . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /build/reproducible-path/vg-1.59.0+ds/lib/libsonlib.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' cd externalTools && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd cutest && make all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c src/gssw.c: In function ‘gssw_sw_software_word’: src/gssw.c:1117:5: warning: ‘__builtin_memcpy’ writing between 18446744069414584336 and 18446744073709551600 bytes into a region of size 9223372036854775807 [-Wstringop-overflow=] 1117 | memcpy(scratch, to_unswizzle, size * sizeof(int16_t)); | ^ In function ‘unswizzle_word’, inlined from ‘gssw_sw_software_word’ at src/gssw.c:1249:9: src/gssw.c:1111:35: note: destination object of size 9223372036854775807 allocated by ‘malloc’ 1111 | int16_t* scratch = (int16_t*) malloc(size * sizeof(int16_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -MF CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o.d -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4975:5: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 4975 | strncpy(n->seq, seq, len); n->seq[len] = 0; | ^ src/gssw.c:4971:19: note: length computed here 4971 | int32_t len = strlen(seq); | ^~~~~~~~~~~ gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c gcc -std=c99 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ [ 12%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -MF CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o.d -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp gcc -std=c99 -Wl,-z,relro -Wl,-z,now -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/config.cpp.o -MF CMakeFiles/sdsl.dir/config.cpp.o.d -o CMakeFiles/sdsl.dir/config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 17%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_metadata.cpp # Make dest directory gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_config.cpp.o -MF CMakeFiles/sdsl.dir/construct_config.cpp.o.d -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_config.cpp gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o -MF CMakeFiles/sdsl.dir/construct_isa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_isa.cpp [ 20%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gssw' . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/build/reproducible-path/vg-1.59.0+ds/include" make libs && cp lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/lib/ && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS && cp src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include/sublinearLS/ make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' rm -f /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin/* /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:765:75: note: declared here 765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:773:68: note: declared here 773 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ /usr/include/lz4.h:774:68: note: declared here 774 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/mutable_path_handle_graph.cpp impl/sonLibConnectivity.c: In function ‘stConnectivity_addEdge’: impl/sonLibConnectivity.c:248:33: warning: pointer ‘component1’ may be used after ‘free’ [-Wuse-after-free] 248 | connectivity->mergeCallback(connectivity->mergeExtraData, component1, component2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘stConnectedComponent_destruct’, inlined from ‘stConnectivity_addEdge’ at impl/sonLibConnectivity.c:238:3: impl/sonLibConnectivity.c:608:9: note: call to ‘free’ here 608 | free(comp); | ^~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 28%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 25%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 31%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/serializable.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 34%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/snarl_decomposition.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 37%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/trivially_serializable.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 40%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/types.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/types.cpp [ 42%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/copy_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibTreap.c: In function ‘stTreap_remove’: impl/sonLibTreap.c:331:18: warning: pointer ‘rmnode’ used after ‘free’ [-Wuse-after-free] 331 | stTreap *p = rmnode->parent; | ^ impl/sonLibTreap.c:329:9: note: call to ‘free’ here 329 | free(rmnode); | ^~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/append_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/are_equivalent.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_tips.cpp rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/topological_sort.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ [ 57%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/apply_orientations.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o [ 60%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -MF CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o.d -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp [ 62%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/count_walks.cpp [ 65%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp mv ../bin/sonLibTests.tmp ../bin/sonLibTests gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm [ 68%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa.cpp mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sonLib' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/build/reproducible-path/vg-1.59.0+ds/include -L. -L/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /build/reproducible-path/vg-1.59.0+ds/lib/ && cp -r src/include/structures /build/reproducible-path/vg-1.59.0+ds/include/ make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/union_find.cpp -o obj/union_find.o ar rc /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/math.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sublinear-Li-Stephens' rm -f lib/cleaned_old_protobuf* rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc rm -Rf include/google/protobuf deps/protobuf touch lib/cleaned_old_protobuf_v003 cp deps/BBHash/BooPHF.h /build/reproducible-path/vg-1.59.0+ds/include cp -r deps/sparsepp/sparsepp include/ rm -Rf include/dynamic.hpp include/dynamic # annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC && rm -Rf build && mkdir -p build && cd build && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make CMake Deprecation Warning at CMakeLists.txt:1 (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. -- Setting build type to 'Release' as none was specified. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63, from /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:8: In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = long int]’, inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:544:23, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:389:19, inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:368:15, inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:738:7, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:445:5: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘’ with nonzero offset [1, 9223372036854775800] [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long int]’, inlined from ‘static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = long int]’ at /usr/include/c++/14/bits/alloc_traits.h:509:28, inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from ‘std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from ‘std::vector<_Tp, _Alloc>::vector(size_type, const value_type&, const allocator_type&) [with _Tp = long int; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:571:47, inlined from ‘std::unordered_map handlegraph::algorithms::dagify(const handlegraph::HandleGraph*, handlegraph::MutableHandleGraph*, size_t)’ at /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dagify.cpp:327:85: /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from ‘void* operator new(std::size_t)’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done Building in Release mode -- Configuring done (1.0s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC -B/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/debug.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 6%] Building CXX object CMakeFiles/debug.dir/debug.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/debug.dir/debug.cpp.o -MF CMakeFiles/debug.dir/debug.cpp.o.d -o CMakeFiles/debug.dir/debug.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/debug.cpp [ 71%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/structures' . ./source_me.sh && cp -r deps/mio/include/mio /build/reproducible-path/vg-1.59.0+ds/include/ . ./source_me.sh && cp -r deps/atomic_queue/include/atomic_queue/* /build/reproducible-path/vg-1.59.0+ds/include/ . ./source_me.sh && cp -r deps/ips4o/ips4o* /build/reproducible-path/vg-1.59.0+ds/include/ cd ./deps/lru_cache && cp *.h* /build/reproducible-path/vg-1.59.0+ds/include/ cp deps/sha1/*.h* /build/reproducible-path/vg-1.59.0+ds/include/ cp deps/progress_bar/progress_bar.hpp /build/reproducible-path/vg-1.59.0+ds/include mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/dozeu && cp deps/dozeu/*.h /build/reproducible-path/vg-1.59.0+ds/include/dozeu/ [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -MF CMakeFiles/sdsl.dir/construct_sa_se.cpp.o.d -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/dijkstra.cpp [ 12%] Linking CXX executable debug /usr/bin/cmake -E cmake_link_script CMakeFiles/debug.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/debug.dir/link.d CMakeFiles/debug.dir/debug.cpp.o -o debug make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 12%] Built target debug make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v1.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 18%] Building CXX object CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -MF CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o.d -o CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/rle_lz77_v1.cpp [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/is_acyclic.cpp [ 37%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -MF CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o.d -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp [ 82%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/reverse_complement.cpp [ 85%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/split_strands.cpp [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/io.cpp.o -MF CMakeFiles/sdsl.dir/io.cpp.o.d -o CMakeFiles/sdsl.dir/io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/io.cpp [ 88%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/chop.cpp [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -MF CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o.d -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o -MF CMakeFiles/sdsl.dir/louds_tree.cpp.o.d -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/louds_tree.cpp [ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/memory_management.cpp.o -MF CMakeFiles/sdsl.dir/memory_management.cpp.o.d -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/memory_management.cpp [ 91%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -MF CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o.d -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -MF CMakeFiles/sdsl.dir/ram_filebuf.cpp.o.d -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp [ 25%] Linking CXX executable rle_lz77_v1 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v1.dir/link.txt --verbose=1 diff: include/vg_environment_version.hpp: No such file or directory . ./source_me.sh && g++ -I -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/progress_bar.o deps/progress_bar/progress_bar.cpp [ 94%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/include -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -std=gnu++14 -fPIC -MD -MT CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -MF CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o.d -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/src/extend.cpp /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/rle_lz77_v1.dir/link.d CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -o rle_lz77_v1 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 25%] Built target rle_lz77_v1 make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v2.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 31%] Building CXX object CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -MF CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o.d -o CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/rle_lz77_v2.cpp g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o -MF CMakeFiles/sdsl.dir/ram_fs.cpp.o.d -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/ram_fs.cpp /usr/bin/g++ -fPIC -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,--dependency-file,CMakeFiles/handlegraph_shared.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/dfs.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_metadata.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/chop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph -B/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake "--color=" ln -s `which shuf` bin/shuf make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/h0_lz77.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 37%] Building CXX object CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -MF CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o.d -o CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/h0_lz77.cpp [ 94%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [ 97%] Built target handlegraph_shared make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[5]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' [100%] Built target handlegraph_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.a -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/serializable.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_position_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/util.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/trivially_serializable.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_mutable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_metadata.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/named_node_back_translation.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/expanding_overlay_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_metadata.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/path_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/types.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/copy_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/reverse_complement.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/chop.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/count_walks.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/extend.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_single_stranded.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/split_strands.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/weakly_connected_components.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/are_equivalent.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/apply_orientations.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dagify.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_tips.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/dijkstra.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/eades_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/is_acyclic.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/strongly_connected_components.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/find_shortest_paths.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/append_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/topological_sort.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/algorithms/internal/dfs.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/deletable_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/mutable_path_handle_graph.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/buildable_snarl_decomposition.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/iteratee.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/handlegraph/snarl_decomposition.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/libhandlegraph/libhandlegraphConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libhandlegraph/build' . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /build/reproducible-path/vg-1.59.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /build/reproducible-path/vg-1.59.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /build/reproducible-path/vg-1.59.0+ds/lib/lib3edgeconnected.a && mkdir -p /build/reproducible-path/vg-1.59.0+ds/include/sonLib && cp lib/*.h /build/reproducible-path/vg-1.59.0+ds/include/sonLib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm [ 62%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -MF CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o.d -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I .//../sonLib/lib/ -c impl/*.c ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /build/reproducible-path/vg-1.59.0+ds/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wl,-z,relro -Wl,-z,now -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o -MF CMakeFiles/sdsl.dir/sd_vector.cpp.o.d -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sd_vector.cpp make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/pinchesAndCacti' rm -f /build/reproducible-path/vg-1.59.0+ds/include/vg.pb.h /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" && export LDFLAGS="-Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=/build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig: cmake -DCMAKE_CXX_STANDARD=14 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;/" -DCMAKE_INSTALL_PREFIX=/build/reproducible-path/vg-1.59.0+ds -DCMAKE_INSTALL_LIBDIR=lib .. && make clean && VERBOSE=1 make && make install -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done [ 43%] Linking CXX executable rle_lz77_v2 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v2.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/rle_lz77_v2.dir/link.d CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -o rle_lz77_v2 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 43%] Built target rle_lz77_v2 make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_bwt.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 50%] Building CXX object CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -MF CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o.d -o CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/rle_bwt.cpp -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Building libvgio for C++ 14 -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Could NOT find Protobuf (missing: Protobuf_DIR) No installed Protobuf has registered itself with CMake. -- Found Protobuf: /usr/lib/aarch64-linux-gnu/libprotobuf.so (found version "3.21.12") Found Protobuf using FindProtobuf.cmake -- Found Threads: TRUE Using real Threads library -- Checking for module 'htslib' -- Found htslib, version 1.20 -- Checking for module 'jansson' -- Found jansson, version 2.14 [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/sfstream.cpp.o -MF CMakeFiles/sdsl.dir/sfstream.cpp.o.d -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/sfstream.cpp Using installed libhandlegraph -- Configuring done (1.6s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/test_libvgio.dir/build.make CMakeFiles/test_libvgio.dir/clean make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -P CMakeFiles/test_libvgio.dir/cmake_clean.cmake make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks [ 56%] Linking CXX executable h0_lz77 make -f CMakeFiles/Makefile2 all /usr/bin/cmake -E cmake_link_script CMakeFiles/h0_lz77.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 2%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out :/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/deps/vg.proto /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/h0_lz77.dir/link.d CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -o h0_lz77 make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 56%] Built target h0_lz77 make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/cw-bwt.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 62%] Building CXX object CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -MF CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o.d -o CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/cw-bwt.cpp [ 5%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/vg.pb.cc.o -MF CMakeFiles/vgio.dir/vg.pb.cc.o.d -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/vg.pb.cc [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/simple_sds.cpp.o -MF CMakeFiles/sdsl.dir/simple_sds.cpp.o.d -o CMakeFiles/sdsl.dir/simple_sds.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/simple_sds.cpp [ 75%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o -MF CMakeFiles/sdsl.dir/structure_tree.cpp.o.d -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/structure_tree.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o -MF CMakeFiles/sdsl.dir/uint128_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint128_t.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o -MF CMakeFiles/sdsl.dir/uint256_t.cpp.o.d -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/util.cpp.o -MF CMakeFiles/sdsl.dir/util.cpp.o.d -o CMakeFiles/sdsl.dir/util.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/util.cpp [ 87%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/../include -I/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -MD -MT lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o -MF CMakeFiles/sdsl.dir/wt_helper.cpp.o.d -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib/wt_helper.cpp [ 68%] Linking CXX executable rle_bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_bwt.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/rle_bwt.dir/link.d CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -o rle_bwt make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 68%] Built target rle_bwt . ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /build/reproducible-path/vg-1.59.0+ds/include/ make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/benchmark.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 75%] Building CXX object CMakeFiles/benchmark.dir/benchmark.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/benchmark.dir/benchmark.cpp.o -MF CMakeFiles/benchmark.dir/benchmark.cpp.o.d -o CMakeFiles/benchmark.dir/benchmark.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/benchmark.cpp [100%] Linking CXX static library libsdsl.a cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/simple_sds.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/build/reproducible-path/vg-1.59.0+ds/include/sdsl/*' rm -f '/build/reproducible-path/vg-1.59.0+ds/lib/libsdsl*' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite -B/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bits.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_comma.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/config.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_config.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_isa.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/csa_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_fully.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/dac_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/enc_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/fast_cache.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/io.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/iterators.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/louds_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/memory_management.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/qsufsort.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/ram_fs.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/raster_img.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rle_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sd_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sfstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/simple_sds.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/structure_tree.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint128_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uint256_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/uintx_t.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/util.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vectors.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wm_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_ap.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_helper.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_huff.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_int.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_pc.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libsdsl.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/build/reproducible-path/vg-1.59.0+ds/include'. The library files are located in '/build/reproducible-path/vg-1.59.0+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! make -f CMakeFiles/wm_string.dir/build.make CMakeFiles/wm_string.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' cd /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles/wm_string.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/wm_string.dir/build.make CMakeFiles/wm_string.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 81%] Building CXX object CMakeFiles/wm_string.dir/wm_string.cpp.o /usr/bin/c++ -I/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -MD -MT CMakeFiles/wm_string.dir/wm_string.cpp.o -MF CMakeFiles/wm_string.dir/wm_string.cpp.o.d -o CMakeFiles/wm_string.dir/wm_string.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/wm_string.cpp [ 87%] Linking CXX executable cw-bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/cw-bwt.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/cw-bwt.dir/link.d "CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o" -o cw-bwt make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [ 87%] Built target cw-bwt make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 8%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/vg.pb.cc.o -MF CMakeFiles/vgio_static.dir/vg.pb.cc.o.d -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/vg.pb.cc [ 11%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 93%] Linking CXX executable benchmark /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 [100%] Linking CXX executable wm_string /usr/bin/cmake -E cmake_link_script CMakeFiles/wm_string.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/benchmark.dir/link.d CMakeFiles/benchmark.dir/benchmark.cpp.o -o benchmark make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [100%] Built target benchmark [ 14%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_emitter.cpp [ 17%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -O3 -DNDEBUG -ggdb -Ofast -fstrict-aliasing -DNDEBUG -march=native -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/wm_string.dir/link.d CMakeFiles/wm_string.dir/wm_string.cpp.o -o wm_string make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' [100%] Built target wm_string make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/build' # Do the copy of the main file last so we can tell if this recipe failed and redo it. # Otherwise we get dynamic.hpp without its deps mkdir -p include/dynamic && cp -r /build/reproducible-path/vg-1.59.0+ds/deps/DYNAMIC/include/dynamic/* include/dynamic/ . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gcsa2 && make directories && make lib/libgcsa2.a && mv lib/libgcsa2.a /build/reproducible-path/vg-1.59.0+ds/lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' mkdir -p bin mkdir -p lib mkdir -p obj make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp [ 20%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -MF CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o.d -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/alignment_io.cpp [ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp [ 26%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/basic_stream.cpp.o -MF CMakeFiles/vgio.dir/src/basic_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/basic_stream.cpp [ 29%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 32%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dbg.o src/dbg.cpp [ 35%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/edit.cpp.o -MF CMakeFiles/vgio.dir/src/edit.cpp.o.d -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/edit.cpp [ 38%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 41%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp [ 44%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_emitter.cpp [ 47%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 50%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 52%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_iterator.cpp [ 55%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/registry.cpp.o -MF CMakeFiles/vgio.dir/src/registry.cpp.o.d -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp [ 58%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/edit.cpp.o -MF CMakeFiles/vgio_static.dir/src/edit.cpp.o.d -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/edit.cpp [ 61%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -MF CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/hfile_cppstream.cpp [ 64%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -MF CMakeFiles/vgio_static.dir/src/json2pb.cpp.o.d -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/json2pb.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp [ 67%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_emitter.cpp [ 70%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream.cpp.o -MF CMakeFiles/vgio.dir/src/stream.cpp.o.d -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream.cpp [ 73%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -MF CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o.d -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/message_iterator.cpp [ 76%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/registry.cpp.o -MF CMakeFiles/vgio_static.dir/src/registry.cpp.o.d -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/registry.cpp [ 79%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 82%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fPIC -fopenmp -MD -MT CMakeFiles/vgio.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp . ./source_me.sh && cp -r deps/gbwt/include/gbwt /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwt && make clean && make && mv lib/libgbwt.a /build/reproducible-path/vg-1.59.0+ds/lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' rm -rf bin lib obj rm -f *.o *.a build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' rm -f test_bwtmerge test_metadata test_queries test_support test_variants *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' mkdir -p bin mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp [ 85%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wl,--dependency-file,CMakeFiles/vgio.dir/link.d -Wl,-z,relro -Wl,-z,now -L/build/reproducible-path/vg-1.59.0+ds/lib -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/lib/aarch64-linux-gnu/libprotobuf.so -lhts -ljansson /build/reproducible-path/vg-1.59.0+ds/lib/libhandlegraph.so make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 85%] Built target vgio /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gcsa.o src/gcsa.cpp [ 88%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/stream.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/bwtmerge.o src/bwtmerge.cpp [ 91%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -MF CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o.d -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/stream_multiplexer.cpp [ 94%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/include -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg -I/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src -isystem /build/reproducible-path/vg-1.59.0+ds/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=gnu++14 -fopenmp -MD -MT CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -MF CMakeFiles/vgio_static.dir/src/vpkg.cpp.o.d -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/src/vpkg.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/lcp.o src/lcp.cpp [ 97%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [100%] Built target vgio_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -S/build/reproducible-path/vg-1.59.0+ds/deps/libvgio -B/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/link_target.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 0%] Built target link_target make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [ 50%] Built target vgio make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' cd /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles/vgio_static.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' [100%] Built target vgio_static make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.so -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/libvgio.a -- Up-to-date: /build/reproducible-path/vg-1.59.0+ds/include -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/json2pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_io.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/fdstream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/loader.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/edit.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/vpkg.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/message_iterator.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/gafkluge.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/basic_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/registry.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/io/alignment_emitter.hpp -- Installing: /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /build/reproducible-path/vg-1.59.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libvgio/build-vg' . ./source_me.sh && rm -Rf /build/reproducible-path/vg-1.59.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/build/reproducible-path/vg-1.59.0+ds/include:/build/reproducible-path/vg-1.59.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" make && cp lib/libbdsg.a /build/reproducible-path/vg-1.59.0+ds/lib && cp -r bdsg/include/* /build/reproducible-path/vg-1.59.0+ds/include make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' [ ! -e bdsg/obj ] || rm -r bdsg/obj [ ! -e lib ] || rm -r lib [ ! -e bin ] || rm -r bin make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/eades_algorithm.cpp -o bdsg/obj/eades_algorithm.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/hash_graph.cpp -o bdsg/obj/hash_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwt.o src/cached_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_graph.o src/path_graph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/dynamic_gbwt.o src/dynamic_gbwt.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/is_single_stranded.cpp -o bdsg/obj/is_single_stranded.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/mapped_structs.cpp -o bdsg/obj/mapped_structs.o rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /build/reproducible-path/vg-1.59.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -DNO_GFAKLUGE -c -o deps/xg/xg.o deps/xg/src/xg.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_graph.cpp -o bdsg/obj/packed_graph.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/fast_locate.o src/fast_locate.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/files.o src/files.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwt.o src/gbwt.cpp ar rcs lib/libgcsa2.a obj/algorithms.o obj/dbg.o obj/files.o obj/gcsa.o obj/internal.o obj/lcp.o obj/path_graph.o obj/support.o obj/utils.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gcsa2' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_position_overlays.cpp -o bdsg/obj/path_position_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_path_position_overlay.cpp -o bdsg/obj/packed_path_position_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/reference_path_overlay.cpp -o bdsg/obj/reference_path_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata.o src/metadata.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_reference_path_overlay.cpp -o bdsg/obj/packed_reference_path_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/path_subgraph_overlay.cpp -o bdsg/obj/path_subgraph_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/subgraph_overlay.cpp -o bdsg/obj/subgraph_overlay.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/support.o src/support.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/vectorizable_overlays.cpp -o bdsg/obj/vectorizable_overlays.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/packed_subgraph_overlay.cpp -o bdsg/obj/packed_subgraph_overlay.o ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/snarl_distance_index.cpp -o bdsg/obj/snarl_distance_index.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/strand_split_overlay.cpp -o bdsg/obj/strand_split_overlay.o g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -O3 -Werror=return-type -std=c++14 -ggdb -g -Ibdsg/include -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c bdsg/src/utility.cpp -o bdsg/obj/utility.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/test.o src/test.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/variants.o src/variants.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_gbwt.o src/build_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/build_ri.o src/build_ri.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/merge_gbwt.o src/merge_gbwt.cpp rm -f lib/libbdsg.a ar rs lib/libbdsg.a bdsg/obj/eades_algorithm.o bdsg/obj/hash_graph.o bdsg/obj/is_single_stranded.o bdsg/obj/mapped_structs.o bdsg/obj/packed_graph.o bdsg/obj/path_position_overlays.o bdsg/obj/packed_path_position_overlay.o bdsg/obj/reference_path_overlay.o bdsg/obj/packed_reference_path_overlay.o bdsg/obj/path_subgraph_overlay.o bdsg/obj/subgraph_overlay.o bdsg/obj/vectorizable_overlays.o bdsg/obj/packed_subgraph_overlay.o bdsg/obj/snarl_distance_index.o bdsg/obj/strand_split_overlay.o bdsg/obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/libbdsg' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/benchmark.o src/benchmark.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/metadata_tool.o src/metadata_tool.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/remove_seq.o src/remove_seq.cpp ar rcs lib/libgbwt.a obj/algorithms.o obj/bwtmerge.o obj/cached_gbwt.o obj/dynamic_gbwt.o obj/fast_locate.o obj/files.o obj/gbwt.o obj/internal.o obj/metadata.o obj/support.o obj/test.o obj/utils.o obj/variants.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_gbwt obj/build_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/build_ri obj/build_ri.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/merge_gbwt obj/merge_gbwt.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/metadata_tool obj/metadata_tool.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/remove_seq obj/remove_seq.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/benchmark obj/benchmark.o lib/libgbwt.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 rm obj/build_ri.o obj/metadata_tool.o obj/benchmark.o obj/merge_gbwt.o obj/remove_seq.o obj/build_gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwt' . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /build/reproducible-path/vg-1.59.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv lib/libgbwtgraph.a /build/reproducible-path/vg-1.59.0+ds/lib make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' rm -rf bin lib obj rm -f *.o *.a gfa2gbwt cd tests && make clean make[4]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' rm -f test_utils test_gbwtgraph test_cached_gbwtgraph test_gfa test_gbz test_minimizer test_index test_algorithms test_path_cover *.o make[4]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph/tests' make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' make[3]: Entering directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' mkdir -p bin mkdir -p lib mkdir -p obj /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/algorithms.o src/algorithms.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/cached_gbwtgraph.o src/cached_gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbwtgraph.o src/gbwtgraph.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz.o src/gbz.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa.o src/gfa.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/internal.o src/internal.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/minimizer.o src/minimizer.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/path_cover.o src/path_cover.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/utils.o src/utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gfa2gbwt.o src/gfa2gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/gbz_stats.o src/gbz_stats.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -c -o obj/kmer_freq.o src/kmer_freq.cpp ar rcs lib/libgbwtgraph.a obj/algorithms.o obj/cached_gbwtgraph.o obj/gbwtgraph.o obj/gbz.o obj/gfa.o obj/internal.o obj/minimizer.o obj/path_cover.o obj/utils.o /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gfa2gbwt obj/gfa2gbwt.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/gbz_stats obj/gbz_stats.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /build/reproducible-path/vg-1.59.0+ds/include -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++14 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/build/reproducible-path/vg-1.59.0+ds/include -o bin/kmer_freq obj/kmer_freq.o lib/libgbwtgraph.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 rm obj/kmer_freq.o obj/gbz_stats.o obj/gfa2gbwt.o make[3]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds/deps/gbwtgraph' . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/back_translating_alignment_emitter.o src/back_translating_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/clip.o src/clip.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/contracting_graph.o src/contracting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/deletion_aligner.o src/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/explainer.o src/explainer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/flat_file_back_translation.o src/flat_file_back_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gbwt_extender.o src/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gbwtgraph_helper.o src/gbwtgraph_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gcsa_helper.o src/gcsa_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/index_registry.o src/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/job_schedule.o src/job_schedule.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/kff.o src/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/kmp.o src/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/mem_accelerator.o src/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/minimizer_mapper_from_chains.o src/minimizer_mapper_from_chains.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/recombinator.o src/recombinator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarl_distance_index.o src/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarl_seed_clusterer.o src/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/sparse_union_find.o src/sparse_union_find.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subpath_overlay.o src/subpath_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/surjecting_alignment_emitter.o src/surjecting_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/traversal_clusters.o src/traversal_clusters.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/zstdutil.o src/zstdutil.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/back_translate.o src/algorithms/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/chain_items.o src/algorithms/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/component.o src/algorithms/component.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/disjoint_components.o src/algorithms/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwt.o src/algorithms/find_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/find_gbwtgraph.o src/algorithms/find_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/find_translation.o src/algorithms/find_translation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/intersect_path_offsets.o src/algorithms/intersect_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/locally_expand_graph.o src/algorithms/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/min_cut_graph.o src/algorithms/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/pad_band.o src/algorithms/pad_band.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/prune.o src/algorithms/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/prune_to_connecting_graph.o src/algorithms/prune_to_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/ref_path_distance.o src/algorithms/ref_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_params_json.o src/io/register_loader_params_json.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbz.o src/io/register_loader_saver_gbz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gbzgraph.o src/io/register_loader_saver_gbzgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_gfa.o src/io/register_loader_saver_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/back_translate.o src/unittest/back_translate.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/chain_items.o src/unittest/chain_items.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/component_paths.o src/unittest/component_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/deletion_aligner.o src/unittest/deletion_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/disjoint_components.o src/unittest/disjoint_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/gbwt_extender.o src/unittest/gbwt_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/index_helpers.o src/unittest/index_helpers.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/index_registry.o src/unittest/index_registry.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/kff.o src/unittest/kff.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/kmp.o src/unittest/kmp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/locally_expand_graph.o src/unittest/locally_expand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/mem_accelerator.o src/unittest/mem_accelerator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/min_cut_graph.o src/unittest/min_cut_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/protobuf.o src/unittest/protobuf.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/sequence_complexity.o src/unittest/sequence_complexity.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/snarl_distance_index.o src/unittest/snarl_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/snarl_seed_clusterer.o src/unittest/snarl_seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/transcriptome.o src/unittest/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/autoindex_main.o src/subcommand/autoindex_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/chain_main.o src/subcommand/chain_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/clip_main.o src/subcommand/clip_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:147:31: required from here 147 | gs.stream_sort(gam_in, cout, index.get()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/any.h:38, from /usr/include/google/protobuf/generated_message_util.h:52, from /build/reproducible-path/vg-1.59.0+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4: /usr/include/google/protobuf/message_lite.h:381:7: note: declared here 381 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/haplotypes_main.o src/subcommand/haplotypes_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/options.o src/subcommand/options.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -MMD -MP -c -o obj/config/allocator_config_jemalloc.o src/config/allocator_config_jemalloc.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/back_translating_alignment_emitter.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/clip.o obj/cluster.o obj/constructor.o obj/contracting_graph.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/deletion_aligner.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/explainer.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flat_file_back_translation.o obj/flow_sort.o obj/funnel.o obj/gbwt_extender.o obj/gbwt_helper.o obj/gbwtgraph_helper.o obj/gcsa_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index_registry.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/job_schedule.o obj/kff.o obj/kmer.o obj/kmp.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/mem_accelerator.o obj/memoizing_graph.o obj/memusage.o obj/minimizer_mapper.o obj/minimizer_mapper_from_chains.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/recombinator.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarl_distance_index.o obj/snarl_seed_clusterer.o obj/snarls.o obj/source_sink_overlay.o obj/sparse_union_find.o obj/splicing.o obj/split_strand_graph.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/subpath_overlay.o obj/surjecting_alignment_emitter.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_clusters.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/zstdutil.o obj/algorithms/alignment_path_offsets.o obj/algorithms/approx_path_distance.o obj/algorithms/back_translate.o obj/algorithms/chain_items.o obj/algorithms/component.o obj/algorithms/coverage_depth.o obj/algorithms/dfs.o obj/algorithms/disjoint_components.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/expand_context.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/find_gbwt.o obj/algorithms/find_gbwtgraph.o obj/algorithms/find_translation.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/intersect_path_offsets.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/locally_expand_graph.o obj/algorithms/merge.o obj/algorithms/min_cut_graph.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/pad_band.o obj/algorithms/path_string.o obj/algorithms/prune.o obj/algorithms/prune_to_connecting_graph.o obj/algorithms/ref_path_distance.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/walk.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_params_json.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gbz.o obj/io/register_loader_saver_gbzgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_gfa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -o test/build_graph test/build_graph.cpp -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/aarch64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic rm -f lib/vg_is_static . ./source_me.sh && g++ -I/usr/include/fastahack -I/build/reproducible-path/vg-1.59.0+ds/include -isystem /build/reproducible-path/vg-1.59.0+ds/include -I. -I/build/reproducible-path/vg-1.59.0+ds/src -I/build/reproducible-path/vg-1.59.0+ds/src/unittest -I/build/reproducible-path/vg-1.59.0+ds/src/unittest/support -I/build/reproducible-path/vg-1.59.0+ds/src/subcommand -I/build/reproducible-path/vg-1.59.0+ds/include/dynamic -I/usr/include/cairo -isystem /usr/include/libpng16 -isystem /usr/include/freetype2 -isystem /usr/include/pixman-1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -O3 -Werror=return-type -ggdb -g -g -O2 -ffile-prefix-map=/build/reproducible-path/vg-1.59.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -o bin/vg obj/main.o obj/unittest/aligner.o obj/unittest/alignment.o obj/unittest/annotation.o obj/unittest/back_translate.o obj/unittest/banded_global_aligner.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/cactus.o obj/unittest/chain_items.o obj/unittest/chunker.o obj/unittest/cluster.o obj/unittest/component_paths.o obj/unittest/constructor.o obj/unittest/copy_graph.o obj/unittest/dagified_graph.o obj/unittest/dagify.o obj/unittest/deletion_aligner.o obj/unittest/dijkstra.o obj/unittest/dinucleotide_machine.o obj/unittest/disjoint_components.o obj/unittest/distributions.o obj/unittest/dozeu_pinning_overlay.o obj/unittest/feature_set.o obj/unittest/flow_sort_test.o obj/unittest/gbwt_extender.o obj/unittest/genome_state.o obj/unittest/genotypekit.o obj/unittest/genotyper.o obj/unittest/gfa.o obj/unittest/handle.o obj/unittest/haplotypes.o obj/unittest/hash_graph.o obj/unittest/hfile_cppstream.o obj/unittest/incremental_subgraph.o obj/unittest/index_helpers.o obj/unittest/index_registry.o obj/unittest/indexed_vg.o obj/unittest/k_widest_paths.o obj/unittest/kff.o obj/unittest/kmp.o obj/unittest/locally_expand_graph.o obj/unittest/mapper.o obj/unittest/mapping.o obj/unittest/mcmc_genotyper.o obj/unittest/mem.o obj/unittest/mem_accelerator.o obj/unittest/min_cut_graph.o obj/unittest/minimizer_mapper.o obj/unittest/msa_converter.o obj/unittest/multipath_alignment.o obj/unittest/multipath_alignment_graph.o obj/unittest/multipath_mapper.o obj/unittest/overlays.o obj/unittest/packed_graph.o obj/unittest/packed_structs.o obj/unittest/path_component_index.o obj/unittest/path_index.o obj/unittest/phase_unfolder.o obj/unittest/phased_genome.o obj/unittest/pinned_alignment.o obj/unittest/position.o obj/unittest/protobuf.o obj/unittest/random_graph.o obj/unittest/readfilter.o obj/unittest/sampler.o obj/unittest/sequence_complexity.o obj/unittest/snarl_distance_index.o obj/unittest/snarl_seed_clusterer.o obj/unittest/snarls.o obj/unittest/source_sink_overlay.o obj/unittest/splicing.o obj/unittest/statistics.o obj/unittest/stream.o obj/unittest/stream_index.o obj/unittest/surject.o obj/unittest/three_edge_connected_components.o obj/unittest/transcriptome.o obj/unittest/traversal_support.o obj/unittest/tree_subgraph.o obj/unittest/variant_adder.o obj/unittest/vcf_buffer.o obj/unittest/vg.o obj/unittest/vg_algorithms.o obj/unittest/vpkg.o obj/unittest/xdrop_aligner.o obj/unittest/xg.o obj/subcommand/add_main.o obj/subcommand/align_main.o obj/subcommand/annotate_main.o obj/subcommand/augment_main.o obj/subcommand/autoindex_main.o obj/subcommand/benchmark_main.o obj/subcommand/call_main.o obj/subcommand/chain_main.o obj/subcommand/chunk_main.o obj/subcommand/circularize_main.o obj/subcommand/clip_main.o obj/subcommand/cluster_main.o obj/subcommand/combine_main.o obj/subcommand/concat_main.o obj/subcommand/construct_main.o obj/subcommand/convert_main.o obj/subcommand/deconstruct_main.o obj/subcommand/depth_main.o obj/subcommand/dotplot_main.o obj/subcommand/explode_main.o obj/subcommand/filter_main.o obj/subcommand/find_main.o obj/subcommand/gamcompare_main.o obj/subcommand/gampcompare_main.o obj/subcommand/gamsort_main.o obj/subcommand/gbwt_main.o obj/subcommand/genotype_main.o obj/subcommand/giraffe_main.o obj/subcommand/haplotypes_main.o obj/subcommand/help_main.o obj/subcommand/ids_main.o obj/subcommand/index_main.o obj/subcommand/inject_main.o obj/subcommand/join_main.o obj/subcommand/kmers_main.o obj/subcommand/map_main.o obj/subcommand/mcmc_main.o obj/subcommand/minimizer_main.o obj/subcommand/mod_main.o obj/subcommand/mpmap_main.o obj/subcommand/msga_main.o obj/subcommand/options.o obj/subcommand/pack_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/rna_main.o obj/subcommand/sift_main.o obj/subcommand/sim_main.o obj/subcommand/simplify_main.o obj/subcommand/snarls_main.o obj/subcommand/sort_main.o obj/subcommand/stats_main.o obj/subcommand/subcommand.o obj/subcommand/surject_main.o obj/subcommand/test_main.o obj/subcommand/trace_main.o obj/subcommand/translate_main.o obj/subcommand/validate_main.o obj/subcommand/vectorize_main.o obj/subcommand/version_main.o obj/subcommand/view_main.o obj/subcommand/viz_main.o obj/config/allocator_config_jemalloc.o -Wl,-z,relro -Wl,-z,now lib/libvg.a -L/build/reproducible-path/vg-1.59.0+ds/lib -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph -lfastahack -lhts -ltabixpp -lcairo -lm -ldl -lz -lz -lm -lz -lfontconfig -lz -lz -lm -lz -lbrotlicommon -lexpat -lm -lfreetype -lz -lbz2 -lpng16 -lz -lm -lz -lbrotlidec -lbrotlicommon -lX11 -lpthread -lxcb -lXau -lXext -lpthread -lxcb -lXau -lXrender -lX11 -lpthread -lxcb -lXau -lX11 -lpthread -lXau -lxcb -lXau -lxcb-render -lxcb -lXau -lxcb-shm -lxcb -lXau -lXdmcp -lpixman-1 -lm -pthread -lzstd -pthread -rdynamic -ldw -lelf -latomic "-lboost_program_options""" -ldl -llzma -lzstd /usr/lib/aarch64-linux-gnu/libjemalloc.a -Wl,-Bstatic -lvgio -lhts -ldeflate -lz -llzma -lprotobuf -lz -ljansson -Wl,-Bdynamic -lpthread -lm make[2]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' cp bin/vg debian/help/ PATH=$PATH:/build/reproducible-path/vg-1.59.0+ds/debian/help \ LD_PRELOAD= help2man \ --no-discard-stderr \ --no-info \ --help-option=help \ --version-option=version \ --name='tools for working with genome variation graphs' \ vg > debian/vg.1 make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' export PATH=$PATH:/build/reproducible-path/vg-1.59.0+ds/debian/help \ && . /build/reproducible-path/vg-1.59.0+ds/source_me.sh \ && ( cd /build/reproducible-path/vg-1.59.0+ds/test && LD_PRELOAD= prove -v t/ ) index file /tmp/vg-K0gDLn/vg-F3bk1G.fai not found, generating... index file /tmp/vg-K0gDLn/vg-tKFWoc.fai not found, generating... index file /tmp/vg-K0gDLn/vg-Jd23fL.fai not found, generating... index file /tmp/vg-K0gDLn/vg-rMiAZ1.fai not found, generating... warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;CIPOS=0,3;CIEND=-3,0 GT ! index file /tmp/vg-K0gDLn/vg-LcGDIo.fai not found, generating... index file /tmp/vg-K0gDLn/vg-k0r6Hb.fai not found, generating... index file /tmp/vg-K0gDLn/vg-whRJXd.fai not found, generating... index file /tmp/vg-K0gDLn/vg-roLcig.fai not found, generating... index file /tmp/vg-K0gDLn/vg-mDxyD8.fai not found, generating... index file /tmp/vg-K0gDLn/vg-greyG6.fai not found, generating... index file /tmp/vg-K0gDLn/vg-MjRBoM.fai not found, generating... index file /tmp/vg-K0gDLn/vg-4CQWPC.fai not found, generating... index file /tmp/vg-K0gDLn/vg-uzKgPT.fai not found, generating... index file /tmp/vg-K0gDLn/vg-JyK1ST.fai not found, generating... Warning: deletion END and SVLEN do not agree [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT END: 29 SVLEN: -19 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT index file /tmp/vg-K0gDLn/vg-qx0vuK.fai not found, generating... Warning: deletion END and SVLEN do not agree [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT END: 29 SVLEN: -19 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=DEL;END=29;SVLEN=-19;CIPOS=0,3;CIEND=-3,0;SPAN=19 GT index file /tmp/vg-K0gDLn/vg-tz3qx4.fai not found, generating... index file /tmp/vg-K0gDLn/vg-9NACjx.fai not found, generating... index file /tmp/vg-K0gDLn/vg-KLqQaQ.fai not found, generating... index file /tmp/vg-K0gDLn/vg-r6oTHT.fai not found, generating... index file /tmp/vg-K0gDLn/vg-K2t8FQ.fai not found, generating... index file /tmp/vg-K0gDLn/vg-1mMFAh.fai not found, generating... index file /tmp/vg-K0gDLn/vg-Kz0Tky.fai not found, generating... index file /tmp/vg-K0gDLn/vg-6uu4cQ.fai not found, generating... index file /tmp/vg-K0gDLn/vg-J91Y5D.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT END: 18 POS: 9 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT index file /tmp/vg-K0gDLn/vg-RYqWmG.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT END: 18 POS: 9 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=18;CIPOS=0,3;SPAN=4 GT index file /tmp/vg-K0gDLn/vg-vtwLmQ.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=13;CIPOS=0,3;SPAN=4 GT END: 13 POS: 9 Warning: VCF writer incorrecty produced END = POS + SVLEN for an insertion. Fixing END to POS. index file /tmp/vg-K0gDLn/vg-XNSipa.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;NA=1;NS=1;SVTYPE=INS;SEQ=ACTG;SVLEN=4;END=13;CIPOS=0,3;SPAN=4 GT END: 13 POS: 9 Warning: VCF writer incorrecty produced END = POS + SVLEN for an insertion. Fixing END to POS. index file /tmp/vg-K0gDLn/vg-F5ZKeO.fai not found, generating... index file /tmp/vg-K0gDLn/vg-zYV748.fai not found, generating... index file /tmp/vg-K0gDLn/vg-MO2XdC.fai not found, generating... index file /tmp/vg-K0gDLn/vg-RdqXAR.fai not found, generating... warning:[vg::Constructor] Lowercase characters found in x; coercing to uppercase. index file /tmp/vg-K0gDLn/vg-0d5mbd.fai not found, generating... warning:[vg::Constructor] Lowercase characters found in x; coercing to uppercase. index file /tmp/vg-K0gDLn/vg-OZGi3I.fai not found, generating... index file /tmp/vg-K0gDLn/vg-Dv1Y8M.fai not found, generating... index file /tmp/vg-K0gDLn/vg-dEkW3p.fai not found, generating... index file /tmp/vg-K0gDLn/vg-1TLxVI.fai not found, generating... 2 0 3 0 iterated on 4 0 iterated on 5 0 iterated on 7 0 iterated on 8 0 iterated on 7 1 Warning: Cactus does not currently support finding snarls in a single-node connected component warning:[GFAParser] Skipping GFA P line: GFA format error: On pass 2: On line 2: Duplicate path x exists in graph Testing libvgio... warning: distance index uses oversized snarls, which may make mapping slow try increasing --snarl-limit when building the distance index warning: distance index uses oversized snarls, which may make mapping slow try increasing --snarl-limit when building the distance index warning: distance index uses oversized snarls, which may make mapping slow try increasing --snarl-limit when building the distance index warning: distance index uses oversized snarls, which may make mapping slow try increasing --snarl-limit when building the distance index 12 11 WARNING: Excluded 2 transcripts with overlapping exons or incorrect exon order. WARNING: Excluded 2 transcripts with overlapping exons or incorrect exon order. WARNING: Excluded 1 transcripts with exon overlapping a haplotype break. t/00_unittest.t ....... 1..1 =============================================================================== All tests passed (8336883 assertions in 617 test cases) ok 1 - vg unit tests complete successfully ok t/01_build_graph.t .... 1..1 ok 1 - graph building with the API ok warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0 ! warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AN=5008;CS=ALU_umary;MEINFO=AluUndef,2,281,+;NS=2504;SVLEN=279;SVTYPE=ALU;TSD=null;DP=18053;EAS_AF=0;AMR_AF=0.0043;AFR_AF=0.0303;EUR_AF=0;SAS_AF=0 ! warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AN=5008;CS=DUP_gs;END=1549769;NS=2504;SVTYPE=DUP;DP=21874;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0.001 ! Warning: deletion END and SVLEN do not agree [canonicalize] z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0;SPAN=3562 END: 1017354 SVLEN: -3562 warning:[vg::Constructor] vcflib could not canonicalize some SVs to base-level sequence; skipping variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0;SPAN=3562 Warning: deletion END and SVLEN do not agree [canonicalize] z 43039 UW_VH_8960 T 100 PASS AC=2;AF=0.000399361;AN=5008;CIEND=0,208;CIPOS=-245,0;CS=DEL_union;END=1044489;NS=2504;SVLEN=-1677;SVTYPE=DEL;DP=18239;EAS_AF=0;AMR_AF=0.0029;AFR_AF=0;EUR_AF=0;SAS_AF=0;SPAN=1677 END: 1044489 SVLEN: -1677 Warning: deletion END and SVLEN do not agree [canonicalize] z 73265 UW_VH_16869 G 100 PASS AC=3;AF=0.000599042;AN=5008;CIEND=0,102;CIPOS=-125,0;CS=DEL_union;END=1077324;NS=2504;SVLEN=-4157;SVTYPE=DEL;DP=19418;EAS_AF=0;AMR_AF=0;AFR_AF=0.0023;EUR_AF=0;SAS_AF=0;SPAN=4157 END: 1077324 SVLEN: -4157 Warning: deletion END and SVLEN do not agree [canonicalize] z 129960 BI_GS_DEL1_B3_P2734_8 A 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-16,16;CIPOS=-16,16;CS=DEL_union;END=1131366;NS=2504;SVLEN=-1405;SVTYPE=DEL;DP=18804;EAS_AF=0;AMR_AF=0;AFR_AF=0.0008;EUR_AF=0;SAS_AF=0;SPAN=1405 END: 1131366 SVLEN: -1405 Warning: deletion END and SVLEN do not agree [canonicalize] z 307697 UW_VH_6096 A 100 PASS AC=2;AF=0.000399361;AN=5008;CIEND=0,82;CIPOS=-77,0;CS=DEL_union;END=1318064;NS=2504;SVLEN=-10447;SVTYPE=DEL;DP=20245;EAS_AF=0.002;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0;SPAN=10447 END: 1318064 SVLEN: -10447 Warning: deletion END and SVLEN do not agree [canonicalize] z 389096 UW_VH_3735 G 100 PASS AC=2647;AF=0.528554;AN=5008;CIEND=0,478;CIPOS=-443,0;CS=DEL_union;END=1390815;NS=2504;SVLEN=-2051;SVTYPE=DEL;DP=18400;EAS_AF=0.7996;AMR_AF=0.5922;AFR_AF=0.2685;EUR_AF=0.5;SAS_AF=0.5849;SPAN=2051 END: 1390815 SVLEN: -2051 Warning: deletion END and SVLEN do not agree [canonicalize] z 405367 BI_GS_DEL1_B3_P2734_19 G 100 PASS AC=2;AF=0.000399361;AN=5008;CIEND=-9,9;CIPOS=-9,9;CS=DEL_union;END=1406601;NS=2504;SVLEN=-1232;SVTYPE=DEL;DP=21506;EAS_AF=0;AMR_AF=0;AFR_AF=0.0015;EUR_AF=0;SAS_AF=0;SPAN=1232 END: 1406601 SVLEN: -1232 Warning: deletion END and SVLEN do not agree [canonicalize] z 557325 UW_VH_21401 G 100 PASS AC=314;AF=0.0626997;AN=5008;CIEND=0,245;CIPOS=-268,0;CS=DEL_union;END=1559946;NS=2504;SVLEN=-2877;SVTYPE=DEL;DP=17241;EAS_AF=0.004;AMR_AF=0.0648;AFR_AF=0.0552;EUR_AF=0.1412;SAS_AF=0.0511;SPAN=2877 END: 1559946 SVLEN: -2877 Warning: deletion END and SVLEN do not agree [canonicalize] z 560739 YL_CN_CHB_4219 T 100 PASS AC=4099;AF=0.81849;AN=5008;CIEND=-500,1000;CIPOS=-1000,500;CS=DEL_union;END=1593685;NS=2504;SVLEN=-32947;SVTYPE=DEL;DP=20713;EAS_AF=0.7867;AMR_AF=0.6527;AFR_AF=0.9213;EUR_AF=0.7903;SAS_AF=0.8589;SPAN=32947 END: 1593685 SVLEN: -32947 Warning: deletion END and SVLEN do not agree [canonicalize] z 596789 BI_GS_DEL1_B1_P2734_566 C 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-11,11;CIPOS=-11,11;CS=DEL_union;END=1600144;NS=2504;SVLEN=-3354;SVTYPE=DEL;DP=16771;EAS_AF=0.001;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0;SPAN=3354 END: 1600144 SVLEN: -3354 Warning: deletion END and SVLEN do not agree [canonicalize] z 599361 BI_GS_DEL1_B2_P2734_449 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-20,20;CIPOS=-20,20;CS=DEL_union;END=1605179;NS=2504;SVLEN=-5817;SVTYPE=DEL;DP=17612;EAS_AF=0;AMR_AF=0;AFR_AF=0.0008;EUR_AF=0;SAS_AF=0;SPAN=5817 END: 1605179 SVLEN: -5817 Warning: deletion END and SVLEN do not agree [canonicalize] z 602412 BI_GS_DEL1_B4_P2734_149 C 100 PASS AC=4;AF=0.000798722;AN=5008;CIEND=-15,15;CIPOS=-15,15;CS=DEL_union;END=1603204;NS=2504;SVLEN=-791;SVTYPE=DEL;DP=21930;EAS_AF=0.002;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0.002;SPAN=791 END: 1603204 SVLEN: -791 Warning: deletion END and SVLEN do not agree [canonicalize] z 670381 UW_VH_15556 T 100 PASS AC=14;AF=0.00279553;AN=5008;CIEND=0,256;CIPOS=-240,0;CS=DEL_union;END=1674237;NS=2504;SVLEN=-4037;SVTYPE=DEL;DP=18965;EAS_AF=0;AMR_AF=0;AFR_AF=0.0106;EUR_AF=0;SAS_AF=0;SPAN=4037 END: 1674237 SVLEN: -4037 Warning: deletion END and SVLEN do not agree [canonicalize] z 995483 UW_VH_2849 T 100 PASS AC=193;AF=0.0385383;AN=5008;CIEND=0,386;CIPOS=-423,0;CS=DEL_union;END=1997552;NS=2504;SVLEN=-2301;SVTYPE=DEL;DP=16520;EAS_AF=0;AMR_AF=0.0461;AFR_AF=0.0454;EUR_AF=0.0547;SAS_AF=0.047;SPAN=2301 END: 1997552 SVLEN: -2301 error:[vg::Constructor] On z, adding reference to last edit end, next end is at 1053404 but reference is only 459552 long warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0 ! warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AN=5008;CS=ALU_umary;MEINFO=AluUndef,2,281,+;NS=2504;SVLEN=279;SVTYPE=ALU;TSD=null;DP=18053;EAS_AF=0;AMR_AF=0.0043;AFR_AF=0.0303;EUR_AF=0;SAS_AF=0 ! Restricting to gi|568815592:29791752-29792749 from 1 to end index file sv/x.fa.fai not found, generating... index file tiny/ambiguous.fa.fai not found, generating... warning:[vg::Constructor] Unsupported IUPAC ambiguity codes found in x; coercing to N. t/02_vg_construct.t ... 1..30 ok 1 - construction produces the right number of nodes ok 2 - construction produces the right number of edges ok 3 - construction obeys rename and region options ok 4 - construction of a 1 megabase graph from the 1000 Genomes succeeds ok 5 - the 1mb graph has the expected number of nodes ok 6 - the 1mb graph has the expected number of edges not ok 7 - vg construct can skip self-inconsistent structural variants # got: '1' # expected: '0' ok 8 - node size is manageable by default ok 9 - construction of a very complex region succeeds ok 10 - the complex graph has the expected number of nodes ok 11 - the complex graph has the expected number of edges ok 12 - the ordering of variants at the same position has no effect on the resulting graph ok 13 - construction does not fail when the first position in the VCF is repeated and has an indel ok 14 - the size of the regions used in construction has no effect on the graph ok 15 - the number of threads used in construction has no effect on the graph ok 16 - the number of threads and regions used in construction has no effect on the graph ok 17 - construction of a graph with two head nodes succeeds ok 18 - the graph contains all the sequence in the reference and VCF ok 19 - varying the max node size does not affect graph length ok 20 - nodes are correctly capped in size ok 21 - -R --region flag is respected ok 22 - vg construct does not require a vcf ok 23 - vg construct respects node size limit ok 24 - --region can be interpreted to be a reference sequence (and not parsed as a region spec) ok 25 - vg constructs the correct graph for inversions ok 26 - vg construct skips variants with . ALTs ok 27 - VCF with * alleles is accepted ok 28 - VCF record with * allele is rejected ok 29 - Reference with ambiguity codes has them coerced to Ns ok 30 - Expected number of Ns are created Failed 1/30 subtests [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. error[VPKG::load_one]: Could not open test/graphs/rgfa_with_reference.rgfa while loading handlegraph::PathHandleGraph error:[get_input_file_name] unable to open input file: test/graphs/rgfa_with_reference.rgfa error[VPKG::load_one]: Could not open test/graphs/rgfa_with_reference.rgfa while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Could not open test/graphs/gfa_with_reference.gfa while loading handlegraph::PathHandleGraph error:[get_input_file_name] unable to open input file: test/graphs/gfa_with_reference.gfa error[VPKG::load_one]: Could not open test/graphs/gfa_with_reference.gfa while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/03_vg_view.t ........ 1..23 ok 1 - view produces the expected number of lines of dot output ok 2 - view produces the expected number of lines of GFA output ok 3 - view converts back and forth between GFA and vg format ok 4 - view can convert BAM to GAM not ok 5 - view can round-trip JSON and GAM # got: '5b9458e2d6d1f262977b932998bb8d3a -' # expected: '7d450e53c0870ff504f33af188613e5d -' ok 6 - view can round-trip qualities and encodes tham as PHRED+0 base-64-encoded strings in JSON Binary files x.vg and - differ not ok 7 - view can reconstruct a VG graph from JSON # got: '1' # expected: '0' ok 8 - view can pass through VG when loading as vg::VG ok 9 - view can pass through semantically identical VG normally ok 10 - view parses sample names ok 11 - view can handle fastq input not ok 12 - unnamed test # got: '4' # expected: 'view can translate graphs with 2-node cycles' ok 13 - view outputs properly oriented GFA ok 14 - view produces the expected number of lines of dot output from a cyclic graph ok 15 - streaming JSON output produces the expected number of chunks ok 16 - duplicate warnings can be suppressed when loading as vg::VG ok 17 - gfa graphs with overlaps are rejected ok 18 - GFA import produces a concise error message when overlaps are present ok 19 - GFA import rejects a GFA file with an overlap that goes beyond its sequences ok 20 - GFA import produces a concise error message in that case ok 21 - vg view preserves path metadata of rGFA file ok 22 - vg view preserves path metadata of GFA file ok 23 - vg view can emit a GFA file with subranges on a haplotype without explicit phase blocks Failed 3/23 subtests [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes t/04_vg_align.t ....... 1..20 ok 1 - alignment traverses the correct path ok 2 - alignment score is as expected ok 3 - full length bonus works and is included by default ok 4 - bonuses are included on only one end for pinned alignments ok 5 - scoring parameters are respected ok 6 - score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected ok 7 - alignment does not contain excessive soft clips under lenient scoring ok 8 - score-matrix file should give same results as --match 2 --mismatch 2: alignment does not contain excessive soft clips under lenient scoring ok 9 - alignment score does not overflow at 255 when using 8x16bit vectors ok 10 - score-matrix file should give same results as --match 2 --mismatch 2: alignment score does not overflow at 255 when using 8x16bit vectors ok 11 - Ns do not cause excessive soft clipping ok 12 - nodes are only referenced if they have mappings ok 13 - align can use query names and outputs GAM ok 14 - alignment to cyclic graphs works ok 15 - graphs where duplicated nodes need flipping can be used for alignment ok 16 - node flipping doesn't destroy the alignment ok 17 - alignment correctly handles an inversion ok 18 - the exploding graph doesn't blow up ok 19 - pinning doesn't cause problems for gssw ok 20 - left pinning is correctly handled ok [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open test.xg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Could not open w.xg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Unreadable stream while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in w.vg while loading handlegraph::PathHandleGraph t/05_vg_find.t ........ 1..29 ok 1 - construction ok 2 - a path can be queried from the xg index ok 3 - a node near another can be obtained using context from the xg index ok 4 - each perfect read contains one maximal exact match ok 5 - vg find -D finds approximate distance between 2 adjacent node starts ok 6 - vg find -D finds approximate distance between node start and adjacent snp ok 7 - vg find -D jumps deletion ok 8 - vg find -D jumps deletion from other allele in snp ok 9 - vg find -L finds same number of nodes (with -c 1) ok 10 - vg find -L works with -r. it scans from start position of first node in range ok 11 - vg find -L tracks length from start position of input node ok 12 - vg find -L works with more than one input node ok 13 - we find the 4 canonical SMEMs from @lh3's bwa mem poster ok 14 - we can find the right MEMs for a sequence with Ns ok 15 - we find the same MEMs sequences with different lengths of Ns ok 16 - the GAM index can return the set of alignments mapping to a node ok 17 - a subgraph query may be used to obtain a particular subset of alignments from a sorted GAM ok 18 - the index can be queried using GAM alignments ok 19 - find gets connected edges between queried nodes by default ok 20 - find gets nodes provided in a node file list not ok 21 - extracting by path adds no extra edges # got: '' # expected: '1' ok 22 - pattern based path extraction works ok 23 - path DAG range query works ok 24 - we can extract a set of targets to separate files ok 25 - the same extraction can be made using BED input ok 26 - we see the expected number of kmers in the given targets ok 27 - we find the expected number of kmers with haplotype frequency equal to 2 ok 28 - GFA i/o for find -n consistent with converting both ways ok 29 - find nodes that map to the provided node ids Failed 1/29 subtests t/06_vg_index.t: line 8: warning: setlocale: LC_ALL: cannot change locale (en_US.utf8): No such file or directory WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. warning: -i option is deprecated WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. t/06_vg_index.t ....... 1..54 ok 1 - building an XG index of a graph ok 2 - building a GCSA index of a graph ok 3 - building both indexes at once ok 4 - the indexes are identical when built one at a time and together ok 5 - building GCSA from XG ok 6 - the GCSA indexes are identical when built from vg and from xg ok 7 - building a GBWT index of a graph with haplotypes ok 8 - building an XG index of a graph with haplotypes ok 9 - xg index does not contain alt paths by default ok 10 - building an XG index of a graph with haplotypes and alt paths included ok 11 - xg index does contains alt paths with index -L ok 12 - building a GCSA index of a graph with haplotypes ok 13 - building all indexes at once ok 14 - the indexes are identical ok 15 - building all indexes at once, while leaving alt paths in xg ok 16 - the indexes are identical with -L ok 17 - xg index does contains alt paths with index -L all at once ok 18 - samples can be excluded from haplotype indexing ok 19 - excluded samples were not included in the GBWT index ok 20 - GBWT from GAF same as from GAM ok 21 - building GBWT index for a regional graph ok 22 - no warnings about missing variants produced ok 23 - building an XG index of multiple graphs ok 24 - building a GCSA index of multiple graphs ok 25 - building both indexes at once ok 26 - the indexes are identical ok 27 - building a GBWT index of multiple graphs with haplotypes ok 28 - building an XG index of multiple graphs with haplotypes ok 29 - building a GCSA index of multiple graphs with haplotypes ok 30 - building XG and GCSA indexes at once ok 31 - building an XG index with alt paths ok 32 - building a GBWT index from an XG index ok 33 - the indexes are identical ok 34 - GBWT can be built for paths ok 35 - fail with nonexistent file ok 36 - a prebuilt deBruijn graph in GCSA2 format may be used ok 37 - vg index and vg gamsort produce identical sorted GAM indexes ok 38 - storage of multiple graphs in an index succeeds ok 39 - can index backward nodes ok 40 - can index kmers for backward nodes ok 41 - GCSA2 index works on cyclic graphs with heads and tails ok 42 - GCSA2 index works on cyclic graphs with no heads or tails ok 43 - GCSA2 index works on cyclic graphs with self loops ok 44 - GCSA2 index works on general cyclic graphs ok 45 - GCSA2 indexing of a tiny graph works ok 46 - GCSA2 indexing succeeds on a single-node graph ok 47 - GCSA2 indexing succeeds on graph with heads but no tails ok 48 - a useful error message is produced when nodes are too large ok 49 - snarl finding with trivial snarls ok 50 - building a distance index of a graph ok 51 - building a distance index of a piped vg graph ok 52 - building a distance index of a piped PackedGraph ok 53 - distance index construction from GBZ ok 54 - distance index construction from piped GBZ ok warning: Thread 0 encountered sequence of length 100, which is longer than the non-chunked limit of 30. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ index file t.fa.fai not found, generating... [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. t/07_vg_map.t ......... 1..55 ok 1 - offset counts unused bases from the start of the node on the forward strand ok 2 - xdrop alignment obtains the expected result ok 3 - xdrop alignment obtains the expected result for the reverse complement ok 4 - score-matrix defaults match 1 mismatch -4 should produce same results: with matrixoffset counts unused bases from the start of the node on the forward strand ok 5 - offset counts unused bases from the start of the node on the reverse strand ok 6 - global alignment traverses the correct path ok 7 - alignment score is as expected ok 8 - scoring parameters are respected ok 9 - score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected ok 10 - full length bonus always be included ok 11 - full length bonus can be set to 0 ok 12 - vg map takes -d as input without a variant graph ok 13 - vg map can align across a SNP ok 14 - alignment works on a small graph ok 15 - binary alignment format is equivalent to json version ok 16 - alignment from BAM correctly handles qualities ok 17 - chunky-banded alignment works ok 18 - multiple alignments are returned in descending score order ok 19 - only a single primary alignment is returned ok 20 - vg can map multi-line FASTA sequences ok 21 - mapping of BAM file produces expected number of alignments ok 22 - mapping from a fastq produces the expected number of alignments ok 23 - allowing secondary alignments with MEM mapping does not change number of primary alignments ok 24 - vg connects paired-end reads in gam output ok 25 - mapping to graphs that can't be oriented without swapping edges works correctly ok 26 - reads multi-map to multiple possible locations ok 27 - vg map works based on gcsa and xg indexes ok 28 - the mapping quality may be capped ok 29 - paired read alignments forced to be consistent have lower score than unrestricted alignments ok 30 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments ok 31 - only primary alignments have mapping quality scores ok 32 - unpaired reads produce mapping quality scores ok 33 - map returns same output on xg and vg (single threaded) ok 34 - base quality adjusted alignment produces higher scores if mismatches have low quality ok 35 - error on vg map -f (unpaired) ok 36 - error on vg map -f (interleaved) ok 37 - error on vg map -f (paired, LHS) ok 38 - error on vg map -f (paired, RHS) ok 39 - mapping a read that touches unused nodes gets the base score ok 40 - mapping a read that matches a haplotype gets a small penalty ok 41 - mapping a read that matches a haplotype with exponent 0 gets the base score ok 42 - mapping a read that matches no haplotypes gets a larger penalty not ok 43 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 44 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 45 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 46 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 47 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '163 # 83' not ok 48 - surjection of unpaired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 49 - surjection of unpaired reads to SAM yields correct pair partner positions # got: '' # expected: '0 # 0' not ok 50 - surjection of unpaired reads to SAM yields distinct QNAMEs # got: '0' # expected: '2' not ok 51 - surjection of unpaired reads to SAM produces absent partner contigs # got: '' # expected: '* # *' not ok 52 - surjection of unpaired reads to SAM produces correct flags # got: '' # expected: '0 # 16' ok 53 - mapper can read FASTA input ok 54 - mapper can read multiline FASTA input ok 55 - xdrop works on a reversed read Failed 10/55 subtests [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. t/08_vg_ids.t ......... 1..10 ok 1 - minimum node as expected (id compaction correct) ok 2 - maximum node is as expected (id compaction correct) ok 3 - correctly generated joint id space for several graphs ok 4 - can sort and re-number a graph with self loops ok 5 - can sort and renumber a complex cyclic graph ok 6 - sorting removes back-edges in a DAG ok 7 - sorting assigns node IDs in topological order ok 8 - sorting does not affect id range ok 9 - sorting does not affect id range of vg ok 10 - sorting does not affect id range of hg ok WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in reversing.vg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in reversing.vg while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'concat' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/09_vg_concat.t ...... 1..4 ok 1 - concat doubles the number of nodes ok 2 - concat doubles the number of edges + 1 ok 3 - concat -p doubles the number of nodes on reversing graph not ok 4 - concat -p doubles the number of edges + 1 on reversing graph # got: '0' # expected: '1' Failed 1/4 subtests t/100_code_quality.t .. 1..1 ok 1 - code quality is acceptable ok warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;END=1017354;NS=2504;SVLEN=-3562;SVTYPE=DEL;DP=15541;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0.001;SAS_AF=0 ! warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AN=5008;CS=ALU_umary;MEINFO=AluUndef,2,281,+;NS=2504;SVLEN=279;SVTYPE=ALU;TSD=null;DP=18053;EAS_AF=0;AMR_AF=0.0043;AFR_AF=0.0303;EUR_AF=0;SAS_AF=0 ! warning:[vg::Constructor] Unsupported variant allele ""; skipping variants like: z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AN=5008;CS=DUP_gs;END=1549769;NS=2504;SVTYPE=DUP;DP=21874;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0.001 ! [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg autoindex] Executing command: vg autoindex -v tiny/tiny.vcf.gz -r tiny/tiny.fa -w giraffe -p tiny [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. warning:[GFAParser] Ignoring unrecognized # line type t/10_vg_stats.t ....... 1..21 ok 1 - vg stats reports the expected number of nodes ok 2 - vg stats reports the expected number of edges ok 3 - vg stats reports the expected graph length ok 4 - vg stats reports the correct number of subgraphs ok 5 - vg stats reports the correct subgraph length ok 6 - distance to head is correct ok 7 - distance to tail is correct ok 8 - aligned read stats are computed correctly ok 9 - basic stats agree between graph formats ok 10 - stats can be computed for GAM files without graphs ok 11 - a path overlap description of a test graph has the expected length ok 12 - vg stats -F detects format of old protobuf graph ok 13 - vg stats -F detects format of newer protobuf graph ok 14 - vg stats -F detects format of hash graph ok 15 - vg stats -F detects format of packed graph ok 16 - vg stats -F detects format of xg graph ok 17 - vg stats -F detects format of GFA graph ok 18 - vg stats -F detects format of GBZ graph ok 19 - vg stats -D found correct degree distribution of tiny graph ok 20 - vg stats -L counts self-loops correctly ok 21 - vg stats -e finds the right nondeterministic edge sets ok WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 68, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 54, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. t/11_vg_paths.t ....... 1..20 ok 1 - path listing works from vg ok 2 - path listing works from XG ok 3 - generic path listing works from XG ok 4 - thread listing works from GBWT ok 5 - haplotype thread listing works from GBWT ok 6 - thread selection by name prefix works correctly ok 7 - thread selection by sample name works correctly ok 8 - no threads are reported for invalid samples ok 9 - vg paths may be used to extract threads ok 10 - vg paths may be used to extract threads as GAF ok 11 - Fasta extracted from xg is the same as the input fasta ok 12 - Fasta extracted from vg is the same as the input fasta ok 13 - Fasta extracted from threads has correct number of lines ok 14 - a single path may be retained ok 15 - path filtering does not modify the graph ok 16 - alt allele paths can be dropped ok 17 - vg path coverage has correct number of columns ok 18 - vg path coverage has correct number of rows ok 19 - vg paths found correct number of lengths ok 20 - vg path coverage reports correct lengths in first column ok WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. warning[vg mod]: -o is deprecated. Dangling edges are now automatically removed. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. t/12_vg_kmers.t ....... 1..10 ok 1 - correct numbers of kmers in the graph ok 2 - to_end edges are handled correctly ok 3 - from_start edges are handled correctly ok 4 - GCSA2 output produces the expected number of lines ok 5 - GCSA2 binary output produces the expected number bytes ok 6 - GCSA2 output works when next position is multiple ok 7 - GCSA2 output works when previous characters are multiple ok 8 - edge-max correctly bounds the number of kmers in a complex graph ok 9 - start/stop node IDs can be specified in GCSA2 output ok 10 - attempting to generate kmers longer than the longest path in a graph correctly yields no kmers ok index file n.fa.fai not found, generating... warning: [HaplotypeIndexer::parse_vcf] contig y not present in file small/x.vcf.gz [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. t/13_vg_sim.t ......... 1..36 ok 1 - vg sim creates the correct number of reads ok 2 - end bonuses are included ok 3 - alignments may be generated rather than read sequences ok 4 - alignments are produced on both strands ok 5 - high simulated error rates do not change the number of bases generated ok 6 - vg sim creates forward-strand reads when asked ok 7 - vg sim can simulate from just a path ok 8 - vg sim can simulate from just a path in FASTQ mode ok 9 - reads can be simulated from all paths ok 10 - simulation was successful ok 11 - reads can be simulated from GBWT samples ok 12 - simulation was successful ok 13 - pairs simulated even when fragments overlap ok 14 - sim does not emit reads with Ns ok 15 - sim can emit reads with Ns when asked to ok 16 - sim doesn't emit Ns even with pair and errors ok 17 - Sample simulation works along with --any-path ok 18 - not having any regexes skips all unvisited contigs ok 19 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs ok 20 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs ok 21 - assigning a ploidy of 0 by regex excludes reads from that contig ok 22 - multiple regexes are interpreted ok 23 - regexes are interpreted as regexes ok 24 - assigning a very high ploidy by regex starves out the other paths ok 25 - Sample simulation works along with --any-path with training FASTQ ok 26 - not having any regexes skips all unvisited contigs with training FASTQ ok 27 - assigning a ploidy of 2 by default gives reads in a ~1-1 ratio vs. diploid covered contigs with training FASTQ ok 28 - assigning a ploidy of 1 by regex gives reads in a ~1-2 ratio vs. diploid covered contigs with training FASTQ ok 29 - assigning a ploidy of 0 by regex excludes reads from that contig with training FASTQ ok 30 - multiple regexes are interpreted with training FASTQ ok 31 - regexes are interpreted as regexes with training FASTQ ok 32 - assigning a very high ploidy by regex starves out the other paths with training FASTQ ok 33 - All reads are annotated with single reference positions by default ok 34 - All reads can be annotated with multiple reference positions when requested ok 35 - ngs trained simulator works ok 36 - ngs trained simulator generates gam ok warning[load_proto_to_graph]: dangling edges on missing node 199474497 and 2 other missing nodes removed [algorithms::normalize] iteration 1 current length 162 [algorithms::normalize] iteration 2 current length 154 [algorithms::normalize] iteration 3 current length 154 [algorithms::normalize] normalized in 2 steps [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. graph: valid [algorithms::normalize] iteration 1 current length 162 [algorithms::normalize] iteration 2 current length 154 [algorithms::normalize] iteration 3 current length 154 [algorithms::normalize] normalized in 2 steps graph: valid graph: valid [algorithms::normalize] iteration 1 current length 162 [algorithms::normalize] iteration 2 current length 154 [algorithms::normalize] iteration 3 current length 154 [algorithms::normalize] normalized in 2 steps [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [algorithms::normalize] iteration 1 current length 95 [algorithms::normalize] iteration 2 current length 95 [algorithms::normalize] normalized in 1 steps [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 100, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 70, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid [algorithms::normalize] iteration 1 current length 5 [algorithms::normalize] normalized in 0 steps graph: valid [algorithms::normalize] iteration 1 current length 5 [algorithms::normalize] normalized in 0 steps graph: valid WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. graph: valid WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'kmers' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. graph: valid graph: valid WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 19. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 19. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 106 [algorithms::normalize] iteration 2 current length 105 [algorithms::normalize] iteration 3 current length 105 [algorithms::normalize] normalized in 2 steps warning: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 103 [algorithms::normalize] iteration 2 current length 100 [algorithms::normalize] iteration 3 current length 100 [algorithms::normalize] normalized in 2 steps t/14_vg_mod.t ......... 1..32 ok 1 - vg mod yields a graph with only a particular path ok 2 - orphan edge removal is automatic ok 3 - graph complexity reduction works as expected ok 4 - short subgraph pruning works ok 5 - normalization produces the correct number of nodes ok 6 - normalization removes redundant SNP alleles ok 7 - normalization produces a valid graph ok 8 - looped normalization produces a valid graph ok 9 - unchop produces a valid graph ok 10 - normalization removes redundant sequence in the graph ok 11 - normalization doesn't introduce cycles and does remove redundancy in bubbles ok 12 - vg mod removes non-path nodes and edge not ok 13 - chopping a graph works correctly with reverse mappings # got: '1' # expected: '0' ok 14 - unchop correctly handles paths ok 15 - unchop correctly handles a graph with an inversion not ok 16 - unchop handles doubly-reversing edges # got: '' # expected: '1' ok 17 - normalization works on a graph with an inversion ok 18 - mod successfully unchops a difficult graph ok 19 - chopping self-cycling nodes retains the cycle ok 20 - unrolling works and produces a valid graph ok 21 - unfolding works and produces a valid graph ok 22 - dagify-unroll produces a graph with the same kmers as the original graph ok 23 - unfold produces a graph with the same kmers as the original graph ok 24 - dagify handles a graph with two strongly connected components ok 25 - unfold followed by dagify produces a graph with no cycles ok 26 - unfold followed by dagify produces a graph with the same kmers as the original graph ok 27 - dagify unrolls the un-unrollable graph ok 28 - sibling simplification does not disrupt paths ok 29 - dagify correctly calculates the minimum distance through the unrolled component ok 30 - dagify produces a graph of the correct size ok 31 - subsetting a flat-alleles graph to a sample graph works ok 32 - removal of high-degree nodes results in the expected number of subgraphs Failed 2/32 subtests warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ warning:[vg mpmap] It is HIGHLY recommended to use a distance index (-d) for clustering on splice graphs. Both accuracy and speed will suffer without one. warning:[vg mpmap] It is HIGHLY recommended to use a distance index (-d) for clustering on splice graphs. Both accuracy and speed will suffer without one. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. index file x.sub.fa.fai not found, generating... warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x x.xg -g x.gcsa -n dna --suppress-mismapping -B -G x.gam -i -F GAM -I 60 -D 10 [vg mpmap] elapsed time 0 s: Loading graph from x.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from x.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from x.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from x.gam using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x x.xg -g x.gcsa -n dna --suppress-mismapping -B -G x.gam -i -F GAMP -I 60 -D 10 [vg mpmap] elapsed time 0 s: Loading graph from x.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from x.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from x.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from x.gam using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 read pairs. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. t/15_vg_surject.t ..... 1..47 ok 1 - reads are generated ok 2 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference ok 3 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference ok 4 - vg surject actually places reads on the correct path ok 5 - vg surject doesn't need to be told which path to use ok 6 - vg surject reports alignment scores not ok 7 - vg surject picks a reference-sense path if it is present # got: '0' # expected: '100' ok 8 - vg surject works for every read simulated from a dense graph ok 9 - vg surject spliced algorithm works for every read simulated from a dense graph ok 10 - vg surject produces valid SAM output ok 11 - vg map may surject reads to produce valid SAM output ok 12 - vg map may surject reads to produce valid BAM output not ok 13 - vg surject retains read names # got: '0' # expected: '100' ok 14 - vg surject can set sample and read group ok 15 - we respect the original mapping's softclips ok 16 - quality strings we will use for testing are oriented correctly ok 17 - forward and reverse orientations of a read produce the same surjected SAM, ignoring flags ok 18 - vg surject produces valid BAM output not ok 19 - mapping quality is preserved through surjection # got: '' # expected: '99' not ok 20 - read pairing is preserved through GAM->GAM surjection # got: '' # expected: 'read/1' ok 21 - interleaved surjection produces same SAM when using GAF and GAM inputs not ok 22 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 23 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 24 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 25 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 26 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '83 # 163' not ok 27 - surjection of paired reads to SAM tags both reads with a read group # got: '0' # expected: '2' not ok 28 - surjection of paired reads to SAM creates RG header # got: '0' # expected: '1' ok 29 - surjection works for a longer (151bp) read ok 30 - surjection works for another difficult read ok 31 - mapping reproduces qualities from BAM input ok 32 - mapping reproduces qualities from fastq input ok 33 - mapping reproduces qualities from GAF input ok 34 - surject works on GAMP input ok 35 - surject works on paired GAMP input ok 36 - vg surject correctly handles subpath suffix in path name ok 37 - vg surject correctly fetches base path length from input file ok 38 - vg surject does not crash when surjecting a read that grazes the reference with a deletion ok 39 - vg surject leaves a read that grazes the reference with a deletion unmapped ok 40 - vg surject does not crash when surjecting a read that grazes the reference with a deletion and pruning low complexity anchors ok 41 - vg surject leaves a read that grazes the reference with a deletion unmapped when pruning low complexity anchors ok 42 - GAM surject can return only primaries ok 43 - GAM surject can return multimappings ok 44 - GAM surject can return paired multimappings ok 45 - GAMP surject can return only primaries ok 46 - GAMP surject can return multimappings ok 47 - GAMP surject can return multimappings Failed 11/47 subtests WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 100 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. could not open msgas/t.fa error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. could not open msgas/t.fa error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 100 [algorithms::normalize] iteration 2 current length 100 [algorithms::normalize] normalized in 1 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file msgas/s-rev.fa.fai not found, generating... warning: Thread 0 encountered sequence of length 100, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 55, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 100 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 49, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file GRCh38_alts/FASTA/HLA/K-3138.fa.fai not found, generating... warning: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3186, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3184, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3183, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3182, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3181, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 64. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file msgas/inv.fa.fai not found, generating... warning: Thread 0 encountered sequence of length 210, which is longer than the non-chunked limit of 20. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 210 [algorithms::normalize] iteration 2 current length 210 [algorithms::normalize] normalized in 1 steps WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 70, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file GRCh38_alts/FASTA/HLA/B-3106.fa.fai not found, generating... warning: Thread 0 encountered sequence of length 3365, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3364, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3343, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3341, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 3340, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 210, which is longer than the non-chunked limit of 16. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. graph: valid t/16_vg_msga.t ........ 1..14 ok 1 - MSGA produces the expected graph for GRCh38 HLA-V ok 2 - X-drop DP MSGA produces the expected graph for GRCh38 HLA-V {"edge": [{"from": "7", "from_start": true, "to": "8", "to_end": true}, {"from": "1", "to": "8"}, {"from": "1", "to": "7"}], "node": [{"id": "7", "sequence": "GGACTAAGGACAAAGGTGCGGGGAG"}, {"id": "8", "sequence": "AACTACTCCACATCAAAGCTACCCAGGCCATTTTAAGTTTCCTGT"}, {"id": "1", "sequence": "TCAGATTCTCATCCCTCCTCAAGGGCTTCT"}], "path": [{"mapping": [{"edit": [{"from_length": 30, "to_length": 30}], "position": {"node_id": "1"}, "rank": "1"}, {"edit": [{"from_length": 45, "to_length": 45}], "position": {"node_id": "8"}, "rank": "2"}, {"edit": [{"from_length": 25, "to_length": 25}], "position": {"node_id": "7"}, "rank": "3"}], "name": "s1"}, {"mapping": [{"edit": [{"from_length": 30, "to_length": 30}], "position": {"node_id": "1"}, "rank": "1"}, {"edit": [{"from_length": 25, "to_length": 25}], "position": {"node_id": "7"}, "rank": "2"}], "name": "s2"}]} ok 3 - soft clips at node boundaries (start) are included correctly ok 4 - soft clips at node boundaries (end) are included correctly ok 5 - region hints (-p) produce same graph ok 6 - adding in existing sequences in reverse doesn't change graph ok 7 - the paths of the graph encode the original sequences used to build it ok 8 - even when banding the paths of the graph encode the original sequences used to build it ok 9 - HLA K-3138 correctly includes all input paths ok 10 - a difficult cyclic path can be included to produce a valid graph ok 11 - a reference sequence set representing an inversion in it may be msga'd and detected ok 12 - edges in cycles with two nodes are correctly included ok 13 - HLA B-3106 is assembled into a valid graph ok 14 - odd-sized overlaps may be used for chunked alignment ok [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ [vg augment] warning: -a / --augmentation-mode option is deprecated error[VPKG::load_one]: Correct input type not found in tiny.vg while loading handlegraph::MutablePathMutableHandleGraph error:[get_input_file_name] unable to open input file: edits-embedded.gam error:[get_input_file] could not open file "edits-embedded.gam" error[VPKG::load_one]: Correct input type not found in augmented.vg while loading handlegraph::PathHandleGraph [vg augment] warning: -a / --augmentation-mode option is deprecated error[VPKG::load_one]: Correct input type not found in tiny.vg while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found in augmented.m1.vg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found in tiny.vg while loading handlegraph::HandleGraph [vg augment] warning: -a / --augmentation-mode option is deprecated error[VPKG::load_one]: Correct input type not found in tiny.vg while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found in augmented.gaf.vg while loading handlegraph::HandleGraph error[VPKG::load_one]: Correct input type not found in augmented.gaf.vg while loading handlegraph::PathHandleGraph terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ [vg augment] warning: -a / --augmentation-mode option is deprecated error[VPKG::load_one]: Correct input type not found in tiny.vg while loading handlegraph::MutablePathMutableHandleGraph error:[get_input_file_name] unable to open input file: edit-embedded.gam error:[get_input_file] could not open file "edit-embedded.gam" error[VPKG::load_one]: Correct input type not found in augmented.vg while loading handlegraph::PathHandleGraph [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes warning: when streaming in a GAM with -A, the output GAM will lose all non-Path related fields from the input [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes t/17_vg_augment.t ..... 1..39 not ok 1 - direct augmentation embeds reads fully for well-supported SNPs # got: '0' # expected: '36' not ok 2 - adding a well-supported SNP by direct augmentation adds 3 more nodes # got: '' # expected: '18' not ok 3 - adding a well-supported SNP by direct augmentation adds 3 more nodes with -m 1 # got: '' # expected: '18' not ok 4 - direct augmentation embeds with GAF reads fully for well-supported SNPs # got: '0' # expected: '36' not ok 5 - adding a well-supported SNP by direct augmentation with GAF adds 3 more nodes # got: '' # expected: '18' not ok 6 - direct augmentation embeds reads fully for probable errors # got: '0' # expected: '3' not ok 7 - adding a probable error by direct augmentation adds 3 more nodes # got: '' # expected: '18' ok 8 - path inclusion does not modify the graph when alignment is a perfect match ok 9 - path inclusion does not modify the graph when alignment has a SNP but doesnt meet the coverage threshold ok 10 - path inclusion does not modify the included path when alignment has a SNP but doesnt meet the coverage threshold ok 11 - output GAM has single edit when SNP was filtered out due to coverage ok 12 - path inclusion with a complex variant introduces the right number of nodes ok 13 - path inclusion works for deletions ok 14 - SNPs can be included in the graph ok 15 - a soft clip at read start becomes a new head of the graph ok 16 - a soft clip at read end becomes a new tail of the graph ok 17 - augment -s works as desired ok 18 - the expected graph translation is exported when the graph is edited ok 19 - editing the graph with many SNP-containing alignments does not introduce duplicate identical nodes ok 20 - augmenting 2 snps with -m 1 produces the same nodes as default ok 21 - augmenting 2 snps and 2 errors with -m 11 produces the same nodes as with just the snps ok 22 - augmenting with 2snps makes correct number of nodes ok 23 - low-quality snp is filtered ok 24 - augmenting a packed graph produces same results as a vg graph ok 25 - augmenting a hash graph produces same results as a vg graph ok 26 - augmenting between nodes without filters works as expected ok 27 - augmenting between nodes with inactive filters works as expected ok 28 - augmenting between nodes N filter works as expected ok 29 - augmenting between nodes without filters works as expected on reverse strand ok 30 - augmenting between nodes with inactive filters works as expected on reverse strand ok 31 - augmenting between nodes N filter works as expected on reverse strand ok 32 - augmenting within node without filters works as expected ok 33 - augmenting within node with inactive filters works as expected ok 34 - augmenting within node with N filter works as expected ok 35 - augmenting within node without filters works as expected on reverse strand ok 36 - augmenting within node with inactive filters works as expected on reverse strand ok 37 - augmenting within node with N filter works as expected on reverse strand ok 38 - sequence in filtered alignment has removed insertion ok 39 - sequence in filtered alignment has removed insertion on reverse strand Failed 7/39 subtests [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in tiny.vg while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open tiny_aug.xg while loading handlegraph::HandleGraph error:[get_input_file_name] unable to open input file: tiny_aug.xg error[VPKG::load_one]: Could not open tiny_aug.xg to determine file type index file inverting/miniFasta.fa.fai not found, generating... WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 200, which is longer than the non-chunked limit of 64. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. index file m.fa.fai not found, generating... [vg autoindex] Executing command: vg autoindex -r small/x.fa -v small/x.vcf.gz -w giraffe -p x [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. index file x_sub1.fa.fai not found, generating... index file x_sub2.fa.fai not found, generating... t/18_vg_call.t ........ 1..19 ok 1 - calling empty gam gives empty VCF ok 2 - Called microinversion ok 3 - Called no microinversion with haploid setting ok 4 - Fewer than 8 differences between called and true SV genotypes ok 5 - Fewer than 8 differences between called haploid and truncated true SV genotypes ok 6 - Same number of reference calls with -a as with -v ok 7 - Calling from extracted traversals by way of GBWT produces same genotypes as calling directly ok 8 - Fewer than 3 differences between allales called via traversals or directly ok 9 - call output same on vg as xg ok 10 - call output same on vg as xg ok 11 - vg call finds true homozygous variants in a cyclic graph ok 12 - vg call finds same variants when using gbwt to enumerate traversals ok 13 - call produces same output with gbwt and gbz ok 14 - vg call makes currect base path header with subpath input ok 15 - vg call makes only currect base path header with subpath input ok 16 - vg call only reports base paths with subpath input ok 17 - vg call makes currect base path header with subpath input and override ok 18 - vg call makes only currect base path header with subpath input and override ok 19 - overriding contig length does not change calls ok t/19_vg_compare.t ..... skipped: (no reason given) rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 85 triples rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 75 triples t/20_vgtordf.t ........ 1..6 ok 1 - vg view produces the expected number of lines of turtle ok 2 - vg view produces the expected number of lines of turtle ok 3 - rapper passed ok 4 - rapper passed ok 5 - vg view produces the expected number of lines of turtle ok 6 - vg view produces the expected number of lines of turtle ok warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x g.xg -g g.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 10 -D 50 -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from g.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from g.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from g.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x g.xg -g g.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 10 -D 1 -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from g.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from g.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from g.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ t/21_vg_filter.t ...... 1..13 ok 1 - vg filter with no options preserves input. ok 2 - vg filter downsamples correctly ok 3 - samtools 1.0+ and vg filter agree on how to select downsampled paired reads ok 4 - samtools 1.0+ and vg filter agree on how to select downsampled unpaired reads ok 5 - reads with refpos annotations not matching an exclusion regex are let through ok 6 - reads with refpos annotations matching an exclusion regex are removed ok 7 - negating a non-filter results in no reads ok 8 - a filter and its complement should form the entire file ok 9 - properly paired read passes proper filter ok 10 - improperly paired read fails proper filter ok 11 - read pairs can be tropped by feature not ok 12 - read pairs can be kept if only one read fails # got: '0' # expected: '2' ok 13 - unmapped reads can be filtered out Failed 1/13 subtests t/22_ggsv.t ........... skipped: (no reason given) t/23_vectorize.t ...... skipped: (no reason given) [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. t/25_circularize.t .... 1..2 ok 1 - a path may be circularized ok 2 - a circular path survives a round trip to/from xg ok WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps Warning [vg deconstruct]: -e is deprecated as it's now on default [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. Warning [vg deconstruct]: -e is deprecated as it's now on default Warning [vg deconstruct]: -e is deprecated as it's now on default [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. Warning [vg deconstruct]: -e is deprecated as it's now on default Warning [vg deconstruct]: -e is deprecated as it's now on default [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. Warning [vg deconstruct]: -e is deprecated as it's now on default [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. Warning [vg deconstruct]: -H is deprecated, and will be ignored Warning [vg deconstruct]: -e is deprecated as it's now on default Warning [vg deconstruct]: -d is deprecated - ploidy now inferred from haplotypes in path names Warning [vg deconstruct]: -H is deprecated, and will be ignored Warning [vg deconstruct]: -e is deprecated as it's now on default Warning [vg deconstruct]: -d is deprecated - ploidy now inferred from haplotypes in path names t/26_deconstruct.t: line 127: bcftools: command not found t/26_deconstruct.t: line 128: bcftools: command not found t/26_deconstruct.t: line 129: bcftools: command not found t/26_deconstruct.t: line 130: bcftools: command not found [vg autoindex] Executing command: vg autoindex -r small/x.fa -v small/x.vcf.gz -w giraffe -p x [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. t/26_deconstruct.t .... 1..37 ok 1 - deconstructed hla vcf has correct number of sites ok 2 - deconstructed hla vcf has correct insertion ok 3 - deconstructed hla vcf with other path has correct number of sites ok 4 - deconstructed hla vcf has correct deletion ok 5 - path-based and exhaustive decontruction give equivalent sites when expected ok 6 - path that differs from reference in every alt has correct genotype ok 7 - path that is same as reference in every alt has correct genotype ok 8 - reference contig correctly written ok 9 - deconstruct correctly handles a simple inversion ok 10 - deconstruct correctly handles a simple inversion when the reference contains the reversing edge ok 11 - deconstruct applies translation from gbz with -O ok 12 - deconstruct correctly handles a cycle in the reference path when contained inside snarl ok 13 - deconstruct correctly handles a cycle in the alt path ok 14 - cyclic reference deconstruction has correct number of variants ok 15 - deconstruct correctly handles cycle in the reference path that spans snarl ok 16 - -P -H options return correct number of variants ok 17 - -P -H options use correct reference name ok 18 - -P -H does not find conflict in alt1 in second variant ok 19 - deconstructing vg graph gives same output as xg graph ok 20 - haplotype 1 preserved when deconstructing small test with gbwt ok 21 - haplotype 2 preserved when deconstructing small test with gbwt ok 22 - gbz deconstruction gives same output as gbwt deconstruction ok 23 - cluster-free deconstruction finds all alt alleles ok 24 - clustered deconstruction finds fewer alt alleles ok 25 - clustered deconstruction finds correct allele info ok 26 - nested deconstruction gets correct star-allele for snp inside deletion ok 27 - PA=0 correctly set at both sites of neseted deletion ok 28 - nested deconstruction gets correct allele for snp inside deletion (without -R) ok 29 - nested deconstruction gets correct allele for snp inside insert ok 30 - PA=0 set for base allele of nested insertion ok 31 - PA=1 set for nested allele of nested insertion ok 32 - nested deconstruction gets correct contigs in vcf header for snp inside insert ok 33 - nested deconstruction gets correct star allele for snp ins2.ide ins2.ert ok 34 - INFO tags correct for level-0 site of double-nested SNP ok 35 - INFO tags correct for level-1 site of double-nested SNP ok 36 - INFO tags correct for level-2 site of double-nested SNP ok 37 - nested deconstruction handles cycle ok Statistics: Number of Non-Degenerate Snarls: 4 Snarls traversed by reads: 4 Snarls on reference: 0 Snarl length distribution: Statistics: Number of Non-Degenerate Snarls: 4 Snarls traversed by reads: 4 Snarls on reference: 4 Snarl length distribution: 2 1 1 3 index file flat1.fa.fai not found, generating... index file flat2.fa.fai not found, generating... Statistics: Number of Non-Degenerate Snarls: 8 Snarls traversed by reads: 8 Snarls on reference: 0 Snarl length distribution: WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. index file flats.fa.fai not found, generating... terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ Warning: realigned read TGTCTGTAGGGC doesn't touch either end of its snarl! Warning: realigned read GGGCTCATTGTA doesn't touch either end of its snarl! Warning: realigned read CTGTAGGGCTCA doesn't touch either end of its snarl! Warning: realigned read GTAGGGCTCATT doesn't touch either end of its snarl! Warning: realigned read CTCATTGTAACG doesn't touch either end of its snarl! Warning: realigned read GCTCATTGTAAC doesn't touch either end of its snarl! Warning: realigned read TATGTCTGTAGG doesn't touch either end of its snarl! Warning: realigned read GCTCATTGTAAC doesn't touch either end of its snarl! Warning: realigned read TTACAATGAGCC doesn't touch either end of its snarl! Warning: realigned read TACAGACATATC doesn't touch either end of its snarl! Warning: realigned read CTGTAGGGCTCA doesn't touch either end of its snarl! Warning: realigned read ACGTTACAATGA doesn't touch either end of its snarl! Warning: realigned read CCCTACAGACAT doesn't touch either end of its snarl! Warning: realigned read TAGGGCTCATTG doesn't touch either end of its snarl! Warning: realigned read GTTACAATGAGC doesn't touch either end of its snarl! Warning: realigned read GTCTGTAGGGCT doesn't touch either end of its snarl! Warning: realigned read GAGCCCTACAGA doesn't touch either end of its snarl! Warning: realigned read GCCCTACAGACA doesn't touch either end of its snarl! Warning: realigned read TGTCTGTAGGGC doesn't touch either end of its snarl! Warning: realigned read ACGTTACAATGA doesn't touch either end of its snarl! Warning: realigned read TACAATGAGCCC doesn't touch either end of its snarl! Warning: realigned read TACAATGAGCCC doesn't touch either end of its snarl! Warning: realigned read AGGGCTCATTGT doesn't touch either end of its snarl! Warning: realigned read CCTACAGACATA doesn't touch either end of its snarl! Warning: realigned read TGAGCCCTACAG doesn't touch either end of its snarl! Statistics: Number of Non-Degenerate Snarls: 1 Snarls traversed by reads: 1 Snarls on reference: 1 Snarl length distribution: 0 1 t/27_vg_genotype.t .... 1..5 ok 1 - vg genotype runs successfully ok 2 - vg genotype runs successfully when emitting vcf ok 3 - called genotypes are correct in a small simulated example ok 4 - genotype format can be converted to and from JSON ok 5 - genotype finds big insert ok terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ [algorithms::normalize] iteration 1 current length 55 [algorithms::normalize] normalized in 0 steps [algorithms::normalize] iteration 1 current length 55 [algorithms::normalize] normalized in 0 steps WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ WARNING:[vg] Subcommand 'translate' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. t/28_translate.t ...... 1..2 ok 1 - alignments used to modify a graph may be projected back to the original graph and used to regenerate the same graph not ok 2 - translation overlay works and produces a sane result # got: '7477871ee13fab8541090e128d02a7f4' # expected: '3ce4390abe667b24eb5148e216a2f5ec' Failed 1/2 subtests [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. warning[vg chunk]: the vg-protobuf format is DEPRECATED. you probably want to use PackedGraph (pg) instead [vg] warning: node ID 44 appears multiple times. Skipping. [vg] warning: node ID 45 appears multiple times. Skipping. [vg] warning: node ID 43 appears multiple times. Skipping. [vg] warning: edge 43 end <-> 44 start appears multiple times. Skipping. [vg] warning: edge 43 end <-> 45 start appears multiple times. Skipping. [vg] warning: node ID 87 appears multiple times. Skipping. [vg] warning: node ID 88 appears multiple times. Skipping. [vg] warning: node ID 85 appears multiple times. Skipping. [vg] warning: node ID 86 appears multiple times. Skipping. [vg] warning: edge 87 end <-> 88 start appears multiple times. Skipping. [vg] warning: edge 85 end <-> 87 start appears multiple times. Skipping. [vg] warning: edge 85 end <-> 86 start appears multiple times. Skipping. [vg] warning: edge 86 end <-> 88 start appears multiple times. Skipping. [vg] warning: node ID 130 appears multiple times. Skipping. [vg] warning: node ID 131 appears multiple times. Skipping. [vg] warning: node ID 129 appears multiple times. Skipping. [vg] warning: edge 130 end <-> 131 start appears multiple times. Skipping. [vg] warning: edge 129 end <-> 130 start appears multiple times. Skipping. [vg] warning: edge 129 end <-> 131 start appears multiple times. Skipping. [vg] warning: node ID 173 appears multiple times. Skipping. [vg] warning: node ID 174 appears multiple times. Skipping. [vg] warning: node ID 172 appears multiple times. Skipping. [vg] warning: edge 173 end <-> 174 start appears multiple times. Skipping. [vg] warning: edge 172 end <-> 173 start appears multiple times. Skipping. [vg] warning: edge 172 end <-> 174 start appears multiple times. Skipping. Restricting to x from 1 to end Restricting to y from 1 to end [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. t/30_vg_chunk.t ....... 1..32 ok 1 - vg chunk with no options preserves nodes ok 2 - vg chunk with no options preserves edges ok 3 - chunk has path going through node 9 ok 4 - chunk can be found from GBZ ok 5 - snarl chunk works on simple example ok 6 - chunk has path going through node 9 ok 7 - -s produces correct number of chunks ok 8 - gam chunker produces correct number of graphs ok 9 - gam chunker produces correct number of gams ok 10 - gam chunker produces bed with correct number of chunks ok 11 - gam chunker emits each matching read at most once ok 12 - chunk contains the expected number of alignments ok 13 - simple gam chunker produces correct number of gams ok 14 - simple chunk contains the expected number of alignments ok 15 - id chunker produces correct chunk size ok 16 - id chunker produces correct single chunk ok 17 - id chunker traces correct chunk size without haplotypes ok 18 - id chunker traces correct chunk size ok 19 - chunker extracts no threads from an empty gPBWT ok 20 - chunker extracts 2 local threads from a gBWT with 2 locally distinct threads in it ok 21 - chunker can extract a partial haplotype from a GBWT ok 22 - chunker can extract a partial haplotype from a GBZ ok 23 - chunker doesn't see haplotypes in the GBZ if asked not to ok 24 - trace consistent on path coordinates ok 25 - n-chunking works and chunks over the full graph ok 26 - path-based components finds subgraphs ok 27 - x gam chunk has correct number of reads ok 28 - y gam chunk has correct number of reads ok 29 - x gam chunk has correct number of reads with -p path ok 30 - y gam chunk has correct number of reads with -p path ok 31 - path-based component contains correct path length ok 32 - components finds subgraphs ok index file add/ref.fa.fai not found, generating... WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. Variant 1: 3 haplotypes at ref:18: 32 bp vs. 33 bp haplotypes vs. graphs average Variant 2: 3 haplotypes at ref:21: 32 bp vs. 34 bp haplotypes vs. graphs average Variant 3: 3 haplotypes at ref:23: 33 bp vs. 34 bp haplotypes vs. graphs average WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. Variant 1: 3 haplotypes at chrR:18: 32 bp vs. 33 bp haplotypes vs. graphs average Variant 2: 3 haplotypes at chrR:21: 32 bp vs. 34 bp haplotypes vs. graphs average Variant 3: 3 haplotypes at chrR:23: 33 bp vs. 34 bp haplotypes vs. graphs average WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. Variant 1: 3 haplotypes at ref:18: 32 bp vs. 33 bp haplotypes vs. graphs average Variant 2: 3 haplotypes at ref:21: 32 bp vs. 34 bp haplotypes vs. graphs average Variant 3: 3 haplotypes at ref:23: 33 bp vs. 34 bp haplotypes vs. graphs average WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. Variant 1: 4 haplotypes at ref:2: 33 bp vs. 34 bp haplotypes vs. graphs average Variant 2: 4 haplotypes at ref:21: 33 bp vs. 36 bp haplotypes vs. graphs average Variant 3: 4 haplotypes at ref:32: 33 bp vs. 36 bp haplotypes vs. graphs average index file add/refN.fa.fai not found, generating... WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. Variant 1: 4 haplotypes at ref:2: 33 bp vs. 34 bp haplotypes vs. graphs average Variant 2: 4 haplotypes at ref:21: 33 bp vs. 36 bp haplotypes vs. graphs average Variant 3: 4 haplotypes at ref:32: 33 bp vs. 36 bp haplotypes vs. graphs average index file add/ngap.fa.fai not found, generating... WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. Variant 1: 2 haplotypes at ngap:10923: 224 bp vs. 224 bp haplotypes vs. graphs average Variant 2: 5 haplotypes at ngap:11014: 256 bp vs. 258 bp haplotypes vs. graphs average Variant 3: 5 haplotypes at ngap:11030: 256 bp vs. 261 bp haplotypes vs. graphs average Variant 4: 5 haplotypes at ngap:11035: 256 bp vs. 261 bp haplotypes vs. graphs average Variant 5: 5 haplotypes at ngap:11043: 256 bp vs. 261 bp haplotypes vs. graphs average WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. Variant 1: 2 haplotypes at x:9: 160 bp vs. 161 bp haplotypes vs. graphs average Variant 2: 2 haplotypes at x:10: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 3: 2 haplotypes at x:14: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 4: 2 haplotypes at x:34: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 5: 2 haplotypes at x:39: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 6: 2 haplotypes at x:52: 224 bp vs. 231 bp haplotypes vs. graphs average Variant 7: 2 haplotypes at x:58: 224 bp vs. 232 bp haplotypes vs. graphs average Variant 8: 2 haplotypes at x:100: 256 bp vs. 265 bp haplotypes vs. graphs average Variant 9: 2 haplotypes at x:103: 256 bp vs. 267 bp haplotypes vs. graphs average Variant 10: 2 haplotypes at x:122: 288 bp vs. 299 bp haplotypes vs. graphs average Variant 11: 2 haplotypes at x:142: 288 bp vs. 301 bp haplotypes vs. graphs average Variant 12: 2 haplotypes at x:160: 306 bp vs. 319 bp haplotypes vs. graphs average Variant 13: 2 haplotypes at x:172: 338 bp vs. 353 bp haplotypes vs. graphs average Variant 14: 2 haplotypes at x:178: 313 bp vs. 327 bp haplotypes vs. graphs average Variant 15: 2 haplotypes at x:187: 313 bp vs. 327 bp haplotypes vs. graphs average Variant 16: 2 haplotypes at x:200: 294 bp vs. 306 bp haplotypes vs. graphs average Variant 17: 2 haplotypes at x:204: 294 bp vs. 306 bp haplotypes vs. graphs average Variant 18: 2 haplotypes at x:218: 288 bp vs. 300 bp haplotypes vs. graphs average Variant 19: 2 haplotypes at x:221: 288 bp vs. 300 bp haplotypes vs. graphs average Variant 20: 2 haplotypes at x:272: 256 bp vs. 266 bp haplotypes vs. graphs average Variant 21: 2 haplotypes at x:277: 256 bp vs. 272 bp haplotypes vs. graphs average Variant 22: 2 haplotypes at x:287: 256 bp vs. 272 bp haplotypes vs. graphs average Variant 23: 2 haplotypes at x:294: 256 bp vs. 272 bp haplotypes vs. graphs average Variant 24: 2 haplotypes at x:297: 291 bp vs. 305 bp haplotypes vs. graphs average Variant 25: 2 haplotypes at x:312: 323 bp vs. 340 bp haplotypes vs. graphs average Variant 26: 2 haplotypes at x:313: 323 bp vs. 341 bp haplotypes vs. graphs average Variant 27: 2 haplotypes at x:345: 291 bp vs. 306 bp haplotypes vs. graphs average Variant 28: 2 haplotypes at x:347: 323 bp vs. 339 bp haplotypes vs. graphs average Variant 29: 2 haplotypes at x:353: 311 bp vs. 326 bp haplotypes vs. graphs average Variant 30: 2 haplotypes at x:373: 291 bp vs. 306 bp haplotypes vs. graphs average Variant 31: 2 haplotypes at x:397: 288 bp vs. 307 bp haplotypes vs. graphs average Variant 32: 2 haplotypes at x:398: 288 bp vs. 307 bp haplotypes vs. graphs average Variant 33: 2 haplotypes at x:405: 241 bp vs. 258 bp haplotypes vs. graphs average Variant 34: 2 haplotypes at x:408: 241 bp vs. 258 bp haplotypes vs. graphs average Variant 35: 2 haplotypes at x:466: 254 bp vs. 260 bp haplotypes vs. graphs average Variant 36: 2 haplotypes at x:474: 286 bp vs. 295 bp haplotypes vs. graphs average Variant 37: 2 haplotypes at x:489: 286 bp vs. 296 bp haplotypes vs. graphs average Variant 38: 2 haplotypes at x:500: 286 bp vs. 297 bp haplotypes vs. graphs average Variant 39: 2 haplotypes at x:523: 300 bp vs. 309 bp haplotypes vs. graphs average Variant 40: 2 haplotypes at x:533: 289 bp vs. 299 bp haplotypes vs. graphs average Variant 41: 1 haplotypes at x:553: 257 bp vs. 263 bp haplotypes vs. graphs average Variant 42: 1 haplotypes at x:566: 257 bp vs. 263 bp haplotypes vs. graphs average Variant 43: 2 haplotypes at x:629: 277 bp vs. 281 bp haplotypes vs. graphs average Variant 44: 2 haplotypes at x:647: 278 bp vs. 285 bp haplotypes vs. graphs average Variant 45: 2 haplotypes at x:654: 278 bp vs. 287 bp haplotypes vs. graphs average Variant 46: 2 haplotypes at x:668: 310 bp vs. 320 bp haplotypes vs. graphs average Variant 47: 2 haplotypes at x:669: 310 bp vs. 321 bp haplotypes vs. graphs average Variant 48: 2 haplotypes at x:681: 289 bp vs. 299 bp haplotypes vs. graphs average Variant 49: 2 haplotypes at x:688: 289 bp vs. 299 bp haplotypes vs. graphs average Variant 50: 2 haplotypes at x:698: 280 bp vs. 289 bp haplotypes vs. graphs average Variant 51: 2 haplotypes at x:714: 299 bp vs. 307 bp haplotypes vs. graphs average Variant 52: 2 haplotypes at x:757: 287 bp vs. 299 bp haplotypes vs. graphs average Variant 53: 2 haplotypes at x:775: 273 bp vs. 285 bp haplotypes vs. graphs average Variant 54: 2 haplotypes at x:777: 273 bp vs. 286 bp haplotypes vs. graphs average Variant 55: 2 haplotypes at x:789: 273 bp vs. 287 bp haplotypes vs. graphs average Variant 56: 2 haplotypes at x:795: 273 bp vs. 287 bp haplotypes vs. graphs average Variant 57: 2 haplotypes at x:813: 287 bp vs. 300 bp haplotypes vs. graphs average Variant 58: 2 haplotypes at x:823: 287 bp vs. 302 bp haplotypes vs. graphs average Variant 59: 2 haplotypes at x:827: 319 bp vs. 334 bp haplotypes vs. graphs average Variant 60: 2 haplotypes at x:858: 297 bp vs. 310 bp haplotypes vs. graphs average Variant 61: 2 haplotypes at x:859: 297 bp vs. 312 bp haplotypes vs. graphs average Variant 62: 2 haplotypes at x:860: 297 bp vs. 312 bp haplotypes vs. graphs average Variant 63: 2 haplotypes at x:877: 287 bp vs. 303 bp haplotypes vs. graphs average Variant 64: 2 haplotypes at x:888: 244 bp vs. 262 bp haplotypes vs. graphs average Variant 65: 2 haplotypes at x:899: 243 bp vs. 263 bp haplotypes vs. graphs average Variant 66: 2 haplotypes at x:901: 243 bp vs. 264 bp haplotypes vs. graphs average Variant 67: 2 haplotypes at x:916: 224 bp vs. 243 bp haplotypes vs. graphs average Variant 68: 2 haplotypes at x:917: 224 bp vs. 243 bp haplotypes vs. graphs average Variant 69: 2 haplotypes at x:923: 223 bp vs. 243 bp haplotypes vs. graphs average Variant 70: 2 haplotypes at x:925: 223 bp vs. 243 bp haplotypes vs. graphs average Variant 71: 2 haplotypes at x:929: 222 bp vs. 242 bp haplotypes vs. graphs average Variant 72: 2 haplotypes at x:939: 204 bp vs. 223 bp haplotypes vs. graphs average Variant 73: 2 haplotypes at x:945: 204 bp vs. 223 bp haplotypes vs. graphs average Variant 74: 2 haplotypes at x:972: 177 bp vs. 194 bp haplotypes vs. graphs average Variant 75: 2 haplotypes at x:1000: 136 bp vs. 149 bp haplotypes vs. graphs average WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ WARNING:[vg] Subcommand 'add' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/31_vg_add.t ......... 1..12 ok 1 - vg add can create a graph ok 2 - vg add can create a graph with contig renames ok 3 - vg add produces the same graph from VCFs with different contig names ok 4 - vg add can create a graph from a PackedGraph ok 5 - vg add produces the same graph from the same input in different formats ok 6 - having reference Ns does not affect the graph topology ok 7 - adding variants adds only the alt bases near large N gaps ok 8 - vg add can create a slightly larger graph ok 9 - ranks are calculated for emitted paths not ok 10 - graphs with backward nodes can be added to # got: '' # expected: '5' not ok 11 - graphs with multiple overlapping paths nodes can be added to # got: '' # expected: '5' not ok 12 - graphs with backward and forward nodes can be added to # got: '' # expected: '5' Failed 3/12 subtests [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in snarls.vg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error:[get_input_file_name] unable to open input file: snarls.xg error[VPKG::load_one]: Could not open snarls.xg while loading handlegraph::PathHandleGraph Restricting to x from 1 to end Restricting to y from 1 to end [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found in nested.vg while loading handlegraph::PathHandleGraph [vg autoindex] Executing command: vg autoindex -p index -g graphs/big_snarl_named.gfa -w giraffe [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing VG graph from GFA input. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Constructing a greedy path cover GBWT [IndexRegistry]: Constructing GBZ using NamedNodeBackTranslation. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. t/32_vg_snarls.t ...... 1..19 not ok 1 - vg snarls made right number of protobuf Snarls # got: '0' # expected: '3' not ok 2 - vg snarls made right number of protobuf SnarlTraversals # got: '0' # expected: '6' not ok 3 - unnamed test # got: '1,3,7,' # expected: 'vg snarls made snarls in the right order' not ok 4 - vg snarls on xg made right number of protobuf Snarls # got: '0' # expected: '3' not ok 5 - vg snarls on xg made right number of protobuf SnarlTraversals # got: '0' # expected: '6' ok 6 - vcf traversals are the same as exhaustive traversals for tiny graph ok 7 - vcf traversals are the same as exhaustive traversals for inversion ok 8 - vcf traversals are the same as exhaustive traversals for ins_and_del graph ok 9 - correct number of snarls when parallelizing on compoents ok 10 - same number of snarls when parallelizing on components ok 11 - GBZ graphs can be used for finding snarls ok 12 - correct number of snarls in the GFA W-line example not ok 13 - vg snarls made the right snarls when dealing with nested chains # got: '1' # expected: '15' not ok 14 - vg snarls made snarls in the right order when dealing with nested chains # got: '1' # expected: '0' ok 15 - Correct snarls are found in GFA space ok 16 - In node ID space traversal visits 7 nodes ok 17 - In node ID space traversal visits 4 trivial snarls ok 18 - In segment name space traversal visits 3 segments ok 19 - In segment name space traversal visits 0 trivial snarls Failed 7/19 subtests [vg mpmap] elapsed time 0 s: Executing command: vg mpmap --suppress-mismapping -B -P 1 -n dna -x xy2.xg -g xy2.gcsa -f reads/xy2.match.fq -F GAM [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.match.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap --suppress-mismapping -B -P 1 -n dna -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.match.fq -F GAM [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0 s: Completed loading GBWT [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.match.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. warning:[vg mpmap] It is HIGHLY recommended to use a distance index (-d) for clustering on splice graphs. Both accuracy and speed will suffer without one. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap --suppress-mismapping -B -M 2 -n rna -x xy2.xg -g xy2.gcsa -f reads/xy2.match.fq [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.match.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -I 200 -D 200 -x xy2.xg -g xy2.gcsa -f reads/xy2.matchpaired.fq -i -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.matchpaired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -I 200 -D 200 -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -f reads/xy2.matchpaired.fq -i -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0 s: Completed loading GBWT [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.matchpaired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. warning:[vg mpmap] Snarl file (-s) is ignored for single path alignment formats (-F) without multipath population scoring (--max-paths). [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -x xy2.xg -g xy2.gcsa -s xy2.snarls -f reads/xy2.discordant.fq -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. warning:[vg mpmap] Snarl file (-s) is ignored for single path alignment formats (-F) without multipath population scoring (--max-paths). [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -x xy2.xg -g xy2.gcsa -s xy2.snarls -f reads/xy2.discordant.fq -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -s xy2.snarls -f reads/xy2.discordant.fq -t 1 -F GAM [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading snarls from xy2.snarls [vg mpmap] elapsed time 0 s: Completed loading snarls [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0 s: Completed loading GBWT [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -P 1 -n dna -x xy2.xg -g xy2.gcsa --gbwt-name xy2.gbwt -s xy2.snarls -f reads/xy2.discordant.fq -t 1 -F GAM [vg mpmap] elapsed time 0 s: Loading graph from xy2.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading snarls from xy2.snarls [vg mpmap] elapsed time 0 s: Completed loading snarls [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy2.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from xy2.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Loading GBWT from xy2.gbwt [vg mpmap] elapsed time 0 s: Completed loading GBWT [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/xy2.discordant.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 10 -D 50 -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -I 100000 -D 5 -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -f reads/grch38_lrc_kir_paired.fq -n dna -B -i -F GAM -t 1 [vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 1 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 1 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 1 s: Completed loading LCP [vg mpmap] elapsed time 1 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1 s: Mapping reads from reads/grch38_lrc_kir_paired.fq using 1 thread warning:[vg mpmap] Could not find 1000 (-b) unambiguous read pair mappings to estimate fragment length ditribution. This can happen due to data issues (e.g. unpaired reads being mapped as pairs) or because the sample size is too large for the read set. Mapping read pairs as independent single-ended reads. [vg mpmap] elapsed time 1 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -x graphs/refonly-lrc_kir.vg.xg -g graphs/refonly-lrc_kir.vg.gcsa -G input.gam -I 500 -D 100 -n dna -i -F GAM --no-qual-adjust [vg mpmap] elapsed time 0 s: Loading graph from graphs/refonly-lrc_kir.vg.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from graphs/refonly-lrc_kir.vg.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from graphs/refonly-lrc_kir.vg.gcsa.lcp [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 1 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 1 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 1 s: Mapping reads from input.gam using 12 threads [vg mpmap] elapsed time 1 s: Mapping finished. Mapped 1000 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -B -n dna -x t.xg -g t.gcsa -f t.fq [vg mpmap] elapsed time 0 s: Loading graph from t.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Loading GCSA2 from t.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from t.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Labeling embedded paths by their connected component [vg mpmap] elapsed time 0 s: Mapping reads from t.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 3 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq [vg mpmap] elapsed time 0 s: Loading graph from s.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 reads. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -i -I 350 -D 10 [vg mpmap] elapsed time 0 s: Loading graph from s.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -i -I 530 -D 10 [vg mpmap] elapsed time 0 s: Loading graph from s.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x s.xg -d s.dist -g s.gcsa -B -n rna -f s.fq -i -I 530 -D 10 -F SAM --report-group-mapq [vg mpmap] elapsed time 0 s: Loading graph from s.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from s.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from s.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from s.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: No reference path file given. Interpreting all non-alt-allele paths in graph as reference sequences. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Mapping reads from s.fq using 12 threads [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 1 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x xy.xg -d xy.dist -g xy.gcsa -G x.gam -F SAM -i --frag-mean 50 --frag-stddev 10 -M 1 [vg mpmap] elapsed time 0 s: Loading graph from xy.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from xy.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from xy.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: No reference path file given. Interpreting all non-alt-allele paths in graph as reference sequences. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Building null model to calibrate mismapping detection [vg mpmap] elapsed time 13 s: Mapping reads from x.gam using 12 threads [vg mpmap] elapsed time 13 s: Mapping finished. Mapped 1000 read pairs. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x xy.xg -d xy.dist -g xy.gcsa -G x.gam -F SAM -M 1 [vg mpmap] elapsed time 0 s: Loading graph from xy.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading GCSA2 from xy.gcsa [vg mpmap] elapsed time 0 s: Loading distance index from xy.dist (in background) [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Loading LCP from xy.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background) [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: No reference path file given. Interpreting all non-alt-allele paths in graph as reference sequences. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg mpmap] elapsed time 0 s: Building null model to calibrate mismapping detection [vg mpmap] elapsed time 16 s: Mapping reads from x.gam using 12 threads [vg mpmap] elapsed time 16 s: Mapping finished. Mapped 2000 reads. t/33_vg_mpmap.t ....... 1..21 ok 1 - MAPQ is 50% without haplotype info ok 2 - haplotype match can disambiguate ok 3 - MAPQs are computed for all multimappings ok 4 - MAPQ is 50% when paired without haplotype info ok 5 - haplotype match can disambiguate paired ok 6 - use of haplotype-aware mapping is recorded ok 7 - Haplotype-oblivious mapping places read on the wrong contig ok 8 - Haplotype-oblivious mapping places read with MAPQ of 50% ok 9 - Haplotype-aware mapping places read on the right contig ok 10 - Haplotype-aware mapping places read with MAPQ > 50% ok 11 - paired read alignments forced to be consistent have lower score than unrestricted alignments ok 12 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments ok 13 - paired read alignments forced to be near each other are closer together in node id space than those forced to be far apart ok 14 - small batches are still all paired in the output ok 15 - multipath mapping works in scenarios that trigger branch point trimming ok 16 - spliced alignments can be found when aligning RNA ok 17 - paired mapping can identify a splice junction on read 1 ok 18 - paired mapping can identify a splice junction on read 2 ok 19 - HTS output contains group mapq annotation ok 20 - paired reads are evenly split between equivalent mappings ok 21 - unpaired reads are evenly split between equivalent mappings ok [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ t/34_vg_pack.t ........ 1..20 ok 1 - allele observation packing detects 2 SNPs ok 2 - pileup packs agree with graph coverage ok 3 - graph coverages are merged from multiple .cx indexes ok 4 - edit records are merged from multiple .cx indexes ok 5 - binned edit accumulation does not affect the result ok 6 - pack records are filtered by node id ok 7 - pack records are filtered by node id ok 8 - pack index merging produces the expected result ok 9 - pack index merging produces the expected result for edges ok 10 - pack computes the same total edge coverage as pileup ok 11 - pack stores the correct edge pileup to disk ok 12 - node packs on vg same as xg ok 13 - edge packs on vg same as xg ok 14 - node packs same on vg when using 3 threads as when using 1 ok 15 - edge packs same on vg when using 2 threads as when using 1 ok 16 - node packs on gaf same as gam ok 17 - edge packs on gaf same as gam not ok 18 - average node qualities are correct # got: '0-0-0-0-0-0-0-0-0-0-' # expected: '20-15-10-10-0-0-0-0-60-60-' ok 19 - pack -s 10 sets fist and last 10bp of coverage to 0 like expected ok 20 - pack -s 9 sets fist and last 9bp of coverage to 0 like expected Failed 1/20 subtests [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open circular_path.xg while loading handlegraph::PathHandleGraph t/36_vg_annotate.t .... 1..9 ok 1 - we can detect when reads contain non-reference variation ok 2 - vg annotate finds the right number of reads overlapping a feature ok 3 - all reads overlapping a feature fall on its node ok 4 - vg annotate finds no reads touching both of two distant features ok 5 - vg annotate shows reads having to go through one feature to get to another at the end ok 6 - vg annotate shows all reads overlapping a whole-reference-covering feature ok 7 - annotating with earliest path position produces one position ok 8 - annotating with multiple path positions produces multiple positions not ok 9 - annotations derived from BED can span the end/start joins of circular paths # got: '' # expected: '{"node_id":"1","offset":"5"} # {"node_id":"1"}' Failed 1/9 subtests t/37_vg_gbwt.t ........ 1..159 ok 1 - chromosome X GBWT with vg gbwt ok 2 - chromosome X GBWT with vg index ok 3 - identical construction results with vg gbwt and vg index ok 4 - chromosome X VCF parse ok 5 - chromosome X GBWT from VCF parse ok 6 - identical construction results with vg gbwt and from VCF parse ok 7 - chromosome X: 2 threads ok 8 - chromosome X: 1 contig ok 9 - chromosome X: 2 haplotypes ok 10 - chromosome X: 1 sample ok 11 - chromosome X: 2 thread names ok 12 - chromosome X: 1 contig name ok 13 - chromosome X: 1 sample name ok 14 - chromosome X reference GBWT with vg gbwt ok 15 - chromosome X reference GBWT with vg index ok 16 - identical construction results with vg gbwt and vg index ok 17 - chromosome X reference: 1 thread ok 18 - chromosome X GAF with vg gbwt ok 19 - chromosome X GAF with vg index ok 20 - identical construction results with vg gbwt and vg index ok 21 - chromosome X GAM with vg gbwt ok 22 - identical construction results from GAF and GAM ok 23 - chromosome X subgraph GBWT with vg gbwt ok 24 - no warnings about missing variants ok 25 - chromosome X subgraph GBWT with vg index ok 26 - identical construction results with vg gbwt and vg index ok 27 - insertion merging with multiple chromosomes ok 28 - fast merging with multiple chromosomes ok 29 - identical merging results with the insertion and fast algorithms ok 30 - parallel merging with multiple chromosomes ok 31 - identical merging results with the insertion and parallel algorithms ok 32 - direct construction with multiple chromosomes and a single VCF ok 33 - identical results with direct construction and merging ok 34 - direct construction with multiple chromosomes and multiple VCFs ok 35 - identical construction results with a single VCF and multiple VCFs ok 36 - construction preset: 1000gp ok 37 - multiple chromosomes: 4 threads ok 38 - multiple chromosomes: 2 contigs ok 39 - multiple chromosomes: 2 haplotypes ok 40 - multiple chromosomes: 1 sample ok 41 - paths as contigs with vg gbwt ok 42 - paths as contigs with vg index ok 43 - identical construction results with vg gbwt and vg index ok 44 - paths as contigs: 2 threads ok 45 - paths as contigs: 2 contigs ok 46 - paths as contigs: 1 haplotype ok 47 - paths as contigs: 1 sample ok 48 - r-index construction ok 49 - normal merging: non-empty + empty ok 50 - the index remains unchanged ok 51 - normal merging: empty + non-empty ok 52 - the index remains unchanged ok 53 - fast merging: non-empty + empty ok 54 - the index remains unchanged ok 55 - fast merging: empty + non-empty ok 56 - the index remains unchanged ok 57 - parallel merging: non-empty + empty ok 58 - the index remains unchanged ok 59 - parallel merging: empty + non-empty ok 60 - the index remains unchanged ok 61 - haplotypes and paths: 6 threads ok 62 - samples can be removed from a GBWT index ok 63 - haplotypes only: 4 threads ok 64 - all samples: 12 threads ok 65 - all samples: 6 haplotypes ok 66 - multiple samples can be removed from a GBWT index ok 67 - sample 2: 4 threads ok 68 - sample 2: 2 haplotypes ok 69 - threads can be extracted from GBWT ok 70 - correct size for the thread file ok 71 - GBWTGraph construction ok 72 - GBWTGraph was serialized correctly ok 73 - GBZ construction from GBWT ok 74 - GBZ was serialized correctly ok 75 - GBZ construction from VCF ok 76 - Identical construction results from GBWT and VCF ok 77 - GBZ construction from GBWTGraph ok 78 - Identical construction results from XG and GBWTGraph ok 79 - GBWT extraction from GBZ ok 80 - Identical GBWT indexes ok 81 - GBWT + GBWTGraph extraction from GBZ ok 82 - Identical GBWT indexes ok 83 - Identical GBWTGraphs ok 84 - Path cover GBWTGraph construction ok 85 - GBWTGraph was serialized correctly ok 86 - path cover: 32 threads ok 87 - path cover: 2 contigs ok 88 - path cover: 16 haplotypes ok 89 - path cover: 16 samples ok 90 - Path cover GBWTGraph construction ok 91 - GBWTGraph was serialized correctly ok 92 - path cover w/ paths: 34 threads ok 93 - path cover w/ paths: 2 contigs ok 94 - path cover w/ paths: 17 haplotypes ok 95 - path cover w/ paths: 17 samples ok 96 - Local haplotypes GBWTGraph construction ok 97 - GBWTGraph was serialized correctly ok 98 - local haplotypes: 32 threads ok 99 - local haplotypes: 2 contigs ok 100 - local haplotypes: 16 haplotypes ok 101 - local haplotypes: 16 samples ok 102 - Local haplotypes GBZ construction (single job) ok 103 - GBZ was serialized correctly ok 104 - Local haplotypes GBZ construction (two jobs) ok 105 - GBZ was serialized correctly ok 106 - Local haplotypes GBWTGraph construction ok 107 - GBWTGraph was serialized correctly ok 108 - local haplotypes w/ paths: 34 threads ok 109 - local haplotypes w/ paths: 2 contigs ok 110 - local haplotypes w/ paths: 17 haplotypes ok 111 - local haplotypes w/ paths: 17 samples ok 112 - Local haplotypes with reference paths from a larger GBZ ok 113 - local haplotypes w/ paths: 36 threads ok 114 - local haplotypes w/ paths: 2 contigs ok 115 - local haplotypes w/ paths: 18 haplotypes ok 116 - local haplotypes w/ paths: 18 samples ok 117 - local haplotypes w/ paths: reference_samples set ok 118 - Augmented GBWTGraph construction ok 119 - GBWTGraph was serialized correctly ok 120 - augmented: 18 threads ok 121 - augmented: 2 contigs ok 122 - augmented: 18 haplotypes ok 123 - augmented: 17 samples ok 124 - GBWT construction from GFA ok 125 - GBWT was serialized correctly ok 126 - gfa: 4 threads ok 127 - gfa: 2 contigs ok 128 - gfa: 2 haplotypes ok 129 - gfa: 1 sample ok 130 - GBWT+GBWTGraph construction from GFA ok 131 - Identical construction results with and without GBWTGraph ok 132 - GBWTGraph was serialized correctly ok 133 - no chopping: 0 translations ok 134 - GBZ construction from GFA ok 135 - GBZ was serialized correctly ok 136 - GBWT+GBWTGraph construction from GFA with chopping ok 137 - chopping: 3 threads ok 138 - chopping: 1 contig ok 139 - chopping: 3 haplotypes ok 140 - chopping: 2 samples ok 141 - chopping: 9 translations ok 142 - Translation can be extracted from GBZ ok 143 - from GBZ: 8 translations ok 144 - GBWT+GBWTGraph construction from GFA with reference paths ok 145 - ref paths: 6 threads ok 146 - ref paths: 2 contigs ok 147 - ref paths: 3 haplotypes ok 148 - ref paths: 2 samples ok 149 - ref paths: 0 translations ok 150 - GBZ construction from GFA with reference ok 151 - GBZ GBWT tag extraction works ok 152 - GBWT tags contain the correct reference samples ok 153 - GBZ GBWT tag modification works ok 154 - Changing reference_samples tag can make a reference a haplotype ok 155 - Changing reference_samples tag can make a haplotype a reference ok 156 - GBZ GBWT tag modification validation works ok 157 - Samples can be direcly set as references ok 158 - Direct reference assignment works ok 159 - GBZ can represent reference paths without haplotype numbers ok t/38_vg_prune.t ....... 1..21 ok 1 - pruning produces the correct number of components ok 2 - pruning leaves the correct number of nodes ok 3 - pruning leaves the correct number of edges ok 4 - pruning without high-degree nodes produces the correct number of components ok 5 - pruning without high-degree nodes leaves the correct number of nodes ok 6 - pruning without high-degree nodes leaves the correct number of edges ok 7 - pruning with path restoring produces the correct number of components ok 8 - pruning with path restoring leaves the correct number of nodes ok 9 - pruning with path restoring leaves the correct number of edges ok 10 - pruning with path/thread unfolding produces the correct number of components ok 11 - pruning with path/thread unfolding produces the correct number of nodes ok 12 - pruning with path/thread unfolding produces the correct number of edges ok 13 - pruning with path unfolding produces the correct number of components ok 14 - pruning with path unfolding produces the correct number of nodes ok 15 - pruning with path unfolding produces the correct number of edges ok 16 - unfolding with multi-chromosome GBWT produces the correct number of components ok 17 - unfolding with multi-chromosome GBWT produces the correct number of nodes ok 18 - unfolding with multi-chromosome GBWT produces the correct number of edges ok 19 - empty mapping starts from the right node id ok 20 - the first unfolded graph adds the correct number of nodes to the mapping ok 21 - the second unfolded graph adds the correct number of nodes to the mapping ok warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. t/39_vg_inject.t ...... 1..14 ok 1 - reads are generated ok 2 - vg inject works for all reads included in the original bam ok 3 - vg inject retains read names ok 4 - vg inject works perfectly for the position of alignment in the simple graph ok 5 - vg inject works perfectly for the position of alignment ok 6 - vg inject works perfectly for the mapping quality of alignment ok 7 - vg inject works perfectly for the cigar of alignment in the simple graph ok 8 - vg inject works perfectly for the cigar of alignment ok 9 - vg inject preserves all reads ok 10 - vg inject works perfectly for the reads flagged as is_reverse ok 11 - vg inject does not make an alignment for an umapped read ok 12 - vg inject does not crash on an unmapped read ok 13 - vg inject supports GAF output ok 14 - vg inject produces valid alignments of the read and reference ok warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. 1000 reads correct 1 reads correct 1 reads correct 0 reads correct 0 reads correct 1 reads correct t/40_vg_gamcompare.t .. 1..7 ok 1 - gamcompare completes ok 2 - gamcompare says the truth is correctly mapped ok 3 - Reads annotated with leftmost position only are close enough at a long distance ok 4 - Reads are close enough at a long distance with a distance index ok 5 - Reads annotated with leftmost position only are too far apart at a short distance ok 6 - Reads are too far apart at a short distance with a distance index ok 7 - Reads annotated with multiple positions only are close enough at a short distance ok Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories Fontconfig error: No writable cache directories [Viz::init] error: Image would be 86252x88 which is larger than the maximum 32,767 px on a side canvas that Cairo supports for raster images. Use an SVG output, try `odgi viz`, or reduce your input size! t/41_vg_viz.t ......... 1..4 ok 1 - vg viz runs ok 2 - vg viz succeeds when drawing a PNG ok 3 - vg viz actually creates an output PNG ok 4 - vg viz knows when a graph is too big to draw as a PNG ok t/42_vg_gamsort.t ..... 1..2 ok 1 - Sorting a GAM orders the alignments by min node ID ok 2 - sorted GAMs can be indexed during the sort ok graph: valid t/43_vg_simplify.t .... 1..5 ok 1 - vg simplify runs through when popping small bubbles ok 2 - simplification pops all the bubbles in a simple graph ok 3 - vg simplify runs through when removing rare variants ok 4 - the graph is valid after removing rare variants ok 5 - simplification keeps only some variants ok t/44_vg_benchmark.t ... 1..1 ok 1 - vg benchmark completes succesfully ok WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. WARNING:[vg] Subcommand 'sort' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. t/45_vg_sort.t ........ 1..5 ok 1 - ids in our test graph are not initially in sorted order ok 2 - a vg graph can be sorted and indexed by ID without crashing ok 3 - a vg graph can be sorted topologically ok 4 - a vg graph can be sorted with Eades algorithm without crashing ok 5 - a vg graph can be sorted with the max-flow algorithm without crashing ok t/46_vg_minimizer.t ... 1..16 ok 1 - default parameters ok 2 - distance index or --no-dist is required ok 3 - single-threaded construction ok 4 - construction is deterministic ok 5 - syncmer index ok 6 - construction is deterministic ok 7 - minimizer parameters ok 8 - setting -k -w works correctly ok 9 - construction from GBWTGraph ok 10 - construction is deterministic ok 11 - construction from GBZ ok 12 - construction is deterministic ok 13 - construction with payload ok 14 - multiple graphs: first ok 15 - multiple graphs: second ok 16 - construction is deterministic ok WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. t/47_vg_dotplot.t ..... 1..1 ok 1 - vg dotplot runs successfully ok [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. warning [vg convert]: currently cannot convert GFA directly to XG; converting through another format terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. warning:[GFAParser] Skipping GFA P line: GFA format error: On pass 1: On line 27: Duplicate path GRCh38.chr1 exists in graph index file ref.fa.fai not found, generating... warning: Thread 11 encountered sequence of length 275, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. alignment: valid graph: valid warning: Thread 0 encountered sequence of length 275, which is longer than the non-chunked limit of 256. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. alignment: valid graph: valid t/48_vg_convert.t ..... 1..106 ok 1 - vg convert maintains same nodes throughout xg conversion ok 2 - vg convert maintains same nodes throughout hash-graph conversion ok 3 - vg convert maintains same nodes throughout packed-graph conversion ok 4 - vg convert maintains same nodes throughout gfa conversion ok 5 - hash graph conversion looks good ok 6 - packed graph conversion looks good ok 7 - vg conversion looks good ok 8 - gfa conversion looks good ok 9 - xg conversion looks good ok 10 - on disk gfa conversion looks good ok 11 - streaming gfa conversion looks good ok 12 - gfa to xg conversion looks good ok 13 - gfa to gfa conversion looks good ok 14 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice ok 15 - vg convert gam -> gaf -> gam -> gaf gives same result multithreaded as with -t 1 ok 16 - vg convert gam -> gaf.gz -> gam -> gaf gives same result multithreaded as with -t 1 ok 17 - vg convert gam -> gaf -> gam produces same gam Paths with snps and indels ok 18 - vg convert gam -> gaf -> gam preserves sequence ok 19 - vg convert gam -> gaf -> gam -> gaf makes same gaf twice in presence of indels and snps ok 20 - vg convert cg-gaf -> gam -> cs-gaf gives expected output (snps converted to matches, insertion converted to Ns) ok 21 - vg convert gam -> gaf -> gam preserves sequences of 1mb1kgp simulated reads ok 22 - vg convert gam -> gaf -> gam ->gaf makes same gaf each time on 1mb1kgp simulated reads not ok 23 - split alignment converted using deletions to represent internal offsets # got: '' # expected: 'cs:Z::13-CCAGTGCTCGCATC:2' ok 24 - vg convert gam -> gaf ->gam -> gaf makes same gaf each time for split alignment ok 25 - convert gam->gaf->gam on softclipped read preserves sequence ok 26 - convert gam->gaf->gam->gaf makes same gaf each time of soft clipped alignment ok 27 - convert gam->gaf->gam on read with floating insertion preserves sequence ok 28 - convert gam->gaf->gam->gaf makes same gaf each time of floating insertion alignment ok 29 - converting gfa and equivalent rgfa produces same output ok 30 - rank-1 rgfa subpath found ok 31 - 2nd column of gfa id translation file contains all rgfa nodes ok 32 - 3rd column of gfa id translation file contains all gfa nodes ok 33 - rgfa output wrote no P-lines ok 34 - rgfa export roundtrips back to normal P-lines ok 35 - GBWTGraph to HashGraph conversion ok 36 - GFA -> GBWTGraph -> HashGraph -> GFA conversion maintains segments ok 37 - GFA -> GBWTGraph -> HashGraph -> GFA conversion maintains walks ok 38 - GBZ to HashGraph conversion ok 39 - GFA -> GBZ -> HashGraph -> GFA conversion maintains segments ok 40 - GBWTGraph to GFA conversion with walks, GBWTGraph algorithm ok 41 - GBWTGraph to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file ok 42 - GBWTGraph to GFA conversion with walks, vg algorithm ok 43 - GBWTGraph to GFA conversion with vg algorithm creates the correct possibly-unnormalized GFA file ok 44 - GBZ to GFA conversion with walks, GBWTGraph algorithm ok 45 - GBZ to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file ok 46 - GFA to HashGraph conversion ok 47 - GFA -> HashGraph -> GFA conversion maintains segments, links, walks, and paths ok 48 - GBWTGraph to HashGraph conversion with generic paths ok 49 - GBWTGraph to HashGraph conversion creates the correct generic paths ok 50 - GBWTGraph to HashGraph conversion creates the correct haplotype paths ok 51 - GBZ to HashGraph conversion with generic paths ok 52 - GBZ to HashGraph conversion creates the correct generic paths ok 53 - GBZ to HashGraph conversion creates the correct haplotype paths ok 54 - GBWTGraph to XG conversion with generic paths ok 55 - GBWTGraph to XG conversion creates the correct generic paths ok 56 - GBWTGraph to XG conversion creates the correct haplotype paths ok 57 - GBZ to XG conversion with generic paths ok 58 - GBZ to XG conversion creates the correct generic paths ok 59 - GBZ to XG conversion creates the correct haplotype paths ok 60 - GBZ to XG conversion while dropping haplotypes ok 61 - No haplotypes in the converted graph ok 62 - GBZ to HashGraph conversion while dropping haplotypes ok 63 - No haplotypes in the converted graph ok 64 - GBWTGraph to GFA conversion with paths and walks, GBWTGraph algorithm ok 65 - GBWTGraph to GFA conversion with GBWTGraph algorithm creates the expected normalized GFA file ok 66 - GBWTGraph to GFA conversion with paths and walks, vg algorithm ok 67 - GBWTGraph to GFA conversion with vg algorithm creates the correct possibly-unnormalized GFA file ok 68 - GBWTGraph to HashGraph conversion with paths and walks ok 69 - HashGraph to GFA conversion with paths and walks ok 70 - GBWTGraph to HashGraph to GFA conversion creates the correct possibly-unnormalized GFA file ok 71 - HashGraph to GFA conversion writing walks as paths ok 72 - HashGraph to GFA conversion writing walks as paths produces no walks ok 73 - HashGraph to GFA conversion writing walks as paths produces all expected paths ok 74 - GBZ to GFA conversion with paths and walks, GBWTGraph algorithm ok 75 - GBZ to GFA conversion with GBWTGraph algorithm creates the correct normalized GFA file ok 76 - GBZ to GFA conversion works with multiple threads ok 77 - GBZ to GFA with translation ok 78 - 8 segments ok 79 - GBZ to GFA without translation ok 80 - 9 segments ok 81 - GFA -> GBZ conversion preserves path metadata ok 82 - GFA -> GBZ -> GFA conversion preserves path metadata ok 83 - GFA -> HashGraph conversion preserves path metadata ok 84 - GFA -> HashGraph -> GFA conversion preserves path metadata ok 85 - rGFA -> HashGraph -> GBZ conversion preserves path metadata ok 86 - rGFA -> HashGraph -> GBZ -> GFA conversion preserves path metadata ok 87 - GFA -> HashGraph conversion works with redundant paths ok 88 - GFA -> HashGraph conversion with redundant paths keeps one copy of the redundant path ok 89 - GFA -> HashGraph conversion works with two-part reference path names ok 90 - GFA -> HashGraph conversion with with two-part reference path names gets the right paths ok 91 - No difference roundtripping a GFA if it's loaded as a GFA or HandleGraph warning:[GFAParser] Streaming GFA file references node 6 before it is defined. GFA lines will be buffered in a temporary file. ok 92 - Streaming an unsorted GFA gives same output as sorted ok 93 - Warning given when falling back to temp GFA buffer file ok 94 - Streaming an sorted GFA gives same output as reading from file ok 95 - No warnings given when streamed GFA is sorted ok 96 - Modding GFA directly produces same output as going through convert ok 97 - Modding sorted GFA stream produces same output as going through convert warning:[GFAParser] Streaming GFA file references node 6 before it is defined. GFA lines will be buffered in a temporary file. ok 98 - Modding unsorted GFA stream produces same output as going through convert ok 99 - Warning given when falling back to temp GFA buffer file in mod ok 100 - Modding unsorted GFA file produces same output as going through convert ok 101 - No warnings given when input GFA file is unsorted ok 102 - rGFA handled consistently when streaming as when loaded from file ok 103 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output (GAF check) ok 104 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output (GAM check) ok 105 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output for long node (GAF check) ok 106 - GAF-GAM double roundtrip works on deletion problem case for chunked vg output for long node (GAM check) Failed 1/106 subtests [vg view] warning: vg-protobuf output (-v / --v) is deprecated. please use vg convert instead. t/49_vg_depth.t ....... 1..6 ok 1 - vg depth gets correct depth from gam ok 2 - vg depth gets correct depth from pack ok 3 - vg depth gets correct number of bins ok 4 - vg depth gets correct depth from gaf ok 5 - vg depth of paths reports all paths ok 6 - vg depth of paths reports just path with selected prefix ok [IndexRegistry]: Constructing GBZ. Guessing that x.gbwt is Giraffe GBWT Guessing that x.xg is XG Guessing that x.xg is XG [IndexRegistry]: Combining Giraffe GBWT and GBWTGraph into GBZ. Guessing that x.gbwt is Giraffe GBWT Guessing that x.xg is XG Guessing that x.gg is GBWTGraph [IndexRegistry]: Constructing minimizer index. Guessing that x.dist is Giraffe Distance Index Guessing that x.gbwt is Giraffe GBWT Guessing that x.min is Minimizers Guessing that x.xg is XG Guessing that x.gg is GBWTGraph Guessing that x.dist is Giraffe Distance Index Guessing that x.gbwt is Giraffe GBWT Guessing that x.min is Minimizers Guessing that x.xg is XG Guessing that x.gg is GBWTGraph Guessing that x.dist is Giraffe Distance Index Guessing that x.gbwt is Giraffe GBWT Guessing that x.min is Minimizers Guessing that x.xg is XG Guessing that x.gg is GBWTGraph Guessing that x.dist is Giraffe Distance Index Guessing that x.gbwt is Giraffe GBWT Guessing that x.min is Minimizers Guessing that x.xg is XG Guessing that x.gg is GBWTGraph [vg minimizer] warning: --bounded-syncmers is deprecated, use --closed-syncmers instead Guessing that x.gg is GBWTGraph Guessing that x.giraffe.gbz is Giraffe GBZ Guessing that x.gg is GBWTGraph Guessing that x.giraffe.gbz is Giraffe GBZ Guessing that x.gg is GBWTGraph Guessing that x.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. index file x.fa.fai not found, generating... [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. [IndexRegistry]: Checking for phasing in VCF(s). Guessing that x.dist is Giraffe Distance Index Guessing that x.min is Minimizers Guessing that x.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that x.dist is Giraffe Distance Index Guessing that x.min is Minimizers Guessing that x.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that x.dist is Giraffe Distance Index Guessing that x.min is Minimizers Guessing that x.giraffe.gbz is Giraffe GBZ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. warning[vg::giraffe]: Finalizing fragment length distribution before reaching maximum sample size mapped 0 reads single ended with 0 pairs of reads left unmapped mean: 0, stdev: 1 [IndexRegistry]: Checking for phasing in VCF(s). Guessing that x.dist is Giraffe Distance Index Guessing that x.min is Minimizers Guessing that x.giraffe.gbz is Giraffe GBZ terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. index file xy.fa.fai not found, generating... [IndexRegistry]: Chunking FASTA(s). [IndexRegistry]: Chunking VCF(s). [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Checking for phasing in VCF(s). Guessing that xy.dist is Giraffe Distance Index Guessing that xy.min is Minimizers Guessing that xy.giraffe.gbz is Giraffe GBZ [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths. [vg autoindex] Executing command: vg autoindex -p brca -w giraffe -g graphs/cactus-BRCA2.gfa [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing VG graph from GFA input. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Constructing a greedy path cover GBWT [IndexRegistry]: Constructing GBZ using NamedNodeBackTranslation. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. [W::bgzf_read_block] EOF marker is absent. The input may be truncated terminate called after throwing an instance of 'std::runtime_error' what(): [vg::io::MessageIterator] obsolete, invalid, or corrupt input at message 79256662206 group 79256662202 ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ [vg autoindex] Executing command: vg autoindex -p 1mb1kgp -w giraffe -P VG w/ Variant Paths:1mb1kgp.vg -P Giraffe Distance Index:1mb1kgp.dist -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Stripping allele paths from VG. [W::bgzf_read_block] EOF marker is absent. The input may be truncated terminate called after throwing an instance of 'std::runtime_error' what(): [vg::io::MessageIterator] obsolete, invalid, or corrupt input at message 79256662206 group 79256662202 ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.59.0 "Casatico" ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Please include this entire error log in your bug report! ━━━━━━━━━━━━━━━━━━━━ error:[vg giraffe] Couldn't open GBZ file 1mb1kgp.giraffe.gbz t/50_vg_giraffe.t ..... 1..50 ok 1 - a read can be mapped with xg + gbwt + min + dist specified without crashing ok 2 - a read can be mapped with gbz + min + dist specified without crashing ok 3 - a read can be mapped with gg + gbwt + min + dist specified without crashing ok 4 - a read can be mapped with the minimizer index being regenerated ok 5 - a read can be mapped with the indexes being inferred by name ok 6 - Mapping logs runtime per read ok 7 - Mapping produces the correct score ok 8 - a read can be mapped with the fast preset ok 9 - a read can be mapped with the default preset ok 10 - Mapping without a full length bonus produces the correct score ok 11 - a read can be mapped with syncmer indexes without crashing ok 12 - a read can be mapped when the distance index is not writable ok 13 - a read which softclips does not appear to loop ok 14 - a read can be mapped with just FASTA and VCF without crashing ok 15 - mapping with just a FASTA and a VCF produced JSON-able alignments ok 16 - mapping to manually-generated indexes and automatically-generated indexes is the same ok 17 - mapping with syncmers produces the same alignment as mapping with minimizers ok 18 - unpaired reads lack cross-references ok 19 - paired reads have cross-references not ok 20 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 21 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 22 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 23 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 24 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '163 # 83' not ok 25 - surjection of unpaired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 26 - surjection of unpaired reads to SAM yields correct pair partner positions # got: '' # expected: '0 # 0' not ok 27 - surjection of unpaired reads to SAM yields distinct QNAMEs # got: '0' # expected: '2' not ok 28 - surjection of unpaired reads to SAM produces absent partner contigs # got: '' # expected: '* # *' not ok 29 - surjection of unpaired reads to SAM produces correct flags # got: '' # expected: '0 # 16' ok 30 - surjecting with a sequence dictionary in non-sorted order produces headers in non-sorted order ok 31 - surjecting with a sequence dictionary in sorted order produces headers in sorted order ok 32 - paired reads are evenly split between equivalent mappings ok 33 - unpaired reads are evenly split between equivalent mappings ok 34 - provenance tracking succeeds for unpaired reads ok 35 - correctness tracking succeeds for unpaired reads ok 36 - unpaired reads are annotated with minimizer coverage ok 37 - provenance tracking succeeds for paired reads ok 38 - correctness tracking succeeds for paired reads ok 39 - paired reads are annotated with minimizer coverage ok 40 - paired reads all have nonzero correct minimizer coverage ok 41 - vg giraffe can map to BAM using a GBZ alone ok 42 - GBZ-based BAM contains the expected number of reads ok 43 - Mapping reads to named coordinates on a nontrivial graph without walks succeeds ok 44 - Reads are all mapped ok 45 - GFA segment names are all set ok 46 - Mapping reads as GAF to named coordinates on a nontrivial graph without walks succeeds ok 47 - Mapping reads as named GAF uses the same names as named GAM not ok 48 - A long read can be correctly aligned # got: '' # expected: '7999' not ok 49 - A long read has the correct edits found # got: '0' # expected: '2' not ok 50 - Long read minimizer set is correctly restricted # got: '0' # expected: '1' Failed 13/50 subtests [vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead. t/51_vg_combine.t ..... 1..10 ok 1 - combined graph as correct total nodes ok 2 - combined graph as correct total edges ok 3 - combined graph has same input path ok 4 - combined handle graph as correct total nodes ok 5 - combined handle graph as correct total edges ok 6 - combined handle graph has same input path ok 7 - path combined graph as correct total nodes ok 8 - path combined path graph as correct total edges ok 9 - path combined graph as correct number of paths ok 10 - combined path has correct size ok rm: cannot remove 'auto.*': No such file or directory [vg autoindex] Executing command: vg autoindex -p auto -w map -r tiny/tiny.fa -v tiny/tiny.vcf.gz --force-unphased [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Pruning complex regions of VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w map -r small/x.fa -v small/x.vcf.gz -r small/y.fa -v small/y.vcf.gz [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. index file small/y.fa.fai not found, generating... [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Pruning complex regions of VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w map -r small/xy.fa -v small/xy2.vcf.gz [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Chunking FASTA(s). [IndexRegistry]: Chunking VCF(s). [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Pruning complex regions of VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r tiny/tiny.fa -v tiny/tiny.vcf.gz -x tiny/tiny.gtf [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from spliced VG. [IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -r tiny/tiny.fa -v tiny/tiny.vcf.gz -x tiny/tiny.gtf --force-unphased [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Finishing spliced VG. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -r tiny/tiny.fa -x tiny/tiny.gtf [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing spliced VG graph from FASTA input. [IndexRegistry]: Finishing spliced VG. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/x.gtf -x small/y.gtf [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from spliced VG. [IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/x.gtf -x small/y.gtf --force-unphased [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Finishing spliced VG. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/xy.gtf [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Chunking FASTA(s). [IndexRegistry]: Chunking VCF(s). [IndexRegistry]: Chunking GTF/GFF(s). [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from spliced VG. [IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -w rpvg -r small/xy.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/xy.gtf [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Chunking FASTA(s). [IndexRegistry]: Chunking VCF(s). [IndexRegistry]: Chunking GTF/GFF(s). [IndexRegistry]: Constructing spliced VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from spliced VG graph and phased VCF input. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Stripping allele paths from spliced VG. [IndexRegistry]: Constructing haplotype-transcript GBWT and finishing spliced VG. [IndexRegistry]: Merging contig GBWTs. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing with GBWT unfolding. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Adding splice junctions to GBZ-format graph. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf -H graphs/gfa_with_w_lines_haplo.gtf [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Adding splice junctions to GBZ-format graph. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg mpmap] elapsed time 0 s: Executing command: vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - [vg mpmap] elapsed time 0 s: Loading graph from auto.spliced.xg [vg mpmap] elapsed time 0 s: Completed loading graph [vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats. [vg mpmap] elapsed time 0 s: Identifying reference paths [vg mpmap] elapsed time 0 s: Loading distance index from auto.spliced.dist [vg mpmap] elapsed time 0 s: Completed loading distance index [vg mpmap] elapsed time 0 s: Loading GCSA2 from auto.spliced.gcsa [vg mpmap] elapsed time 0 s: Completed loading GCSA2 [vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries [vg mpmap] elapsed time 0 s: Loading LCP from auto.spliced.gcsa.lcp [vg mpmap] elapsed time 0 s: Completed loading LCP [vg mpmap] elapsed time 0 s: Mapping reads from STDIN using 1 thread [vg mpmap] elapsed time 0 s: Mapping finished. Mapped 20 reads. [vg autoindex] Executing command: vg autoindex -p auto -w rpvg -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Constructing haplotype-transcript GBWT and spliced graph from GBZ-format graph. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w rpvg -w mpmap -g graphs/gfa_with_w_lines.gfa -x graphs/gfa_with_w_lines.gtf -H graphs/gfa_with_w_lines_haplo.gtf [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Constructing haplotype-transcript GBWT and spliced graph from GBZ-format graph. [IndexRegistry]: Joining transcript origin table. [IndexRegistry]: Constructing spliced XG graph from spliced VG graph. [IndexRegistry]: Constructing distance index for a spliced graph. [IndexRegistry]: Pruning complex regions of spliced VG to prepare for GCSA indexing. [IndexRegistry]: Constructing GCSA/LCP indexes. [vg autoindex] Executing command: vg autoindex -p auto -w giraffe -r tiny/tiny.fa -v tiny/tiny.vcf.gz [IndexRegistry]: Checking for phasing in VCF(s). [IndexRegistry]: Chunking inputs for parallelism. [IndexRegistry]: Constructing VG graph from FASTA and VCF input. [IndexRegistry]: Constructing GBWT from VG graph and phased VCF input. [IndexRegistry]: Stripping allele paths from VG. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Downsampling full GBWT. [IndexRegistry]: Not too many haplotypes; augmenting the full GBWT instead. [IndexRegistry]: Constructing GBZ. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. [vg autoindex] Executing command: vg autoindex -p auto -w giraffe -g graphs/gfa_with_w_lines.gfa [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. warning [vg convert]: currently cannot convert GFA directly to XG; converting through another format [vg autoindex] Executing command: vg autoindex -p auto -w giraffe -g graphs/named_with_walk.gfa [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing a GBZ from GFA input. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. [vg autoindex] Executing command: vg autoindex -p auto -w giraffe -g graphs/named.gfa [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing VG graph from GFA input. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Constructing a greedy path cover GBWT [IndexRegistry]: Constructing GBZ using NamedNodeBackTranslation. [IndexRegistry]: Constructing distance index for Giraffe. [IndexRegistry]: Constructing minimizer index. t/52_vg_autoindex.t ... 1..49 ok 1 - autoindexing successfully completes indexing for vg map with basic input ok 2 - autoindexing makes 3 outputs for vg map ok 3 - autoindexing makes an XG for vg map ok 4 - autoindexing makes a GCSA2/LCP pair for vg map ok 5 - basic autoindexing results can be used by vg map ok 6 - autoindexing successfully completes indexing for vg map with chunked input ok 7 - chunked autoindexing results can be used by vg map ok 8 - autoindexing successfully completes indexing for vg map with phased input ok 9 - phased autoindexing results can be used by vg map ok 10 - autoindexing successfully completes indexing for vg mpmap with unchunked input ok 11 - autoindexing creates 6 files for mpmap/rpvg ok 12 - basic autoindexing results can be used by vg mpmap ok 13 - haplotype transcript GBWT made by autoindex is valid ok 14 - transcript origin table has expected number of rows ok 15 - autoindexing successfully completes indexing for vg mpmap with unchunked, unphased input ok 16 - autoindexing creates 4 files for mpmap/rpvg ok 17 - basic unphased autoindexing results can be used by vg mpmap ok 18 - autoindexing successfully completes indexing for vg mpmap without variants ok 19 - autoindexing creates 4 files for mpmap without variants ok 20 - autoindexing results with no variants can be used by vg mpmap ok 21 - autoindexing successfully completes indexing for vg mpmap with chunked input ok 22 - autoindexing creates 6 files for mpmap/rpvg with chunked input ok 23 - autoindexing successfully completes indexing for vg mpmap with unphased chunked input ok 24 - autoindexing creates 4 files for mpmap/rpvg with chunked input ok 25 - autoindexing results with chunked unphased input can be used by vg mpmap ok 26 - autoindexing successfully completes indexing for vg mpmap with partially chunked input ok 27 - autoindexing successfully completes indexing for vg mpmap with another partially chunked input ok 28 - autoindexing successfully completes indexing for vg mpmap with GFA input ok 29 - autoindexing results with GFA input can be used by vg mpmap ok 30 - autoindexing successfully completes indexing for vg mpmap with GFA input and a haplotype GTF ok 31 - autoindexing results with GFA input and a haplotype GTF can be used by vg mpmap ok 32 - autoindexing successfully completes indexing for vg mpmap and rpvg with GFA input ok 33 - autoindexing successfully completes indexing for vg mpmap and rpvg with GFA input and a haplotype GTF ok 34 - autoindexing successfully completes indexing for vg giraffe with unchunked input ok 35 - autoindexing creates 3 inputs for vg giraffe ok 36 - basic autoindexing results can be used by vg giraffe ok 37 - autoindexing successfully completes indexing for vg giraffe with GFA input with W-lines ok 38 - autoindexing creates 3 inputs for vg giraffe from GFA input ok 39 - GFA autoindexing results can be used by vg giraffe ok 40 - autoindexing successfully completes on a GFA with named segments and W-lines ok 41 - GFA segment names are available in output GAM when a walk exists ok 42 - autoindexing successfully completes on a GFA with named segments and no W-lines ok 43 - GFA segment names are available in output GAM when no walks exist ok 44 - Running out of room during k-mer enumeration triggers a rewind ok 45 - Indexing is successful after rewinding from k-mer generation ok 46 - Running out of room during GCSA2 indexing triggers a rewind ok 47 - Indexing is successful after rewinding from GCSA2 indexing ok 48 - Running out of memory during GCSA2 indexing triggers a rewind ok 49 - Indexing is successful after rewinding from GCSA2 indexing ok WARNING:[vg] Subcommand 'msga' is deprecated and is no longer being actively maintained. Future releases may eliminate it entirely. !!! WARNING !!! vg msga was an early prototype for constructing genome graphs from multiple sequence alignments, but it is no longer state-of-the-art or even actively maintained. VG team members have developed improved graph construction algorithms in Cactus and PGGB, and several other tools have been developed by other groups. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 998, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. warning: Thread 0 encountered sequence of length 975, which is longer than the non-chunked limit of 128. Alignments may be discontiguous. To adjust this behavior, change the band width parameter. Suppressing further warnings. [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps graph: valid graph: valid graph: valid graph: valid graph: valid graph: valid t/53_clip.t ........... 1..17 ok 1 - clipped graph is valid ok 2 - every step in clipped graph belongs to reference path ok 3 - clipped graph has same length as ref path ok 4 - clipped graph is valid ok 5 - Just one node filtered ok 6 - clipped graph is valid ok 7 - Just one edge filtered ok 8 - clipped graph is valid ok 9 - Just one node filtered ok 10 - clipped graph is valid ok 11 - clipping bad region changes nothing ok 12 - clipped graph is valid ok 13 - Just one node filtered ok 14 - stub clipping removed all stubs ok 15 - region clipping filtered out only 2 / 4 stub nodes ok 16 - Correct head after path stubbification ok 17 - Correct tail after path stubbification ok t/54_vg_haplotypes.t .. 1..21 ok 1 - generating haplotype information ok 2 - sampling from existing haplotype information ok 3 - 1 generated + 2 reference samples ok 4 - 2 contigs ok 5 - 4 generated + 2 reference haplotypes ok 6 - sampling the haplotypes directly ok 7 - the outputs are identical ok 8 - sampling without adding reference ok 9 - 1 sample ok 10 - 2 contigs ok 11 - 4 haplotypes ok 12 - diploid sampling ok 13 - 1 generated + 2 reference samples ok 14 - 2 contigs ok 15 - 2 generated + 2 reference haplotypes ok 16 - diploid sampling using a preset ok 17 - the outputs are identical ok 18 - Giraffe integration with a guessed output name ok 19 - the sampled graph is identical to a manually sampled one ok 20 - Giraffe integration with a specified output name ok 21 - the sampled graphs are identical ok Test Summary Report ------------------- t/02_vg_construct.t (Wstat: 0 Tests: 30 Failed: 1) Failed test: 7 t/03_vg_view.t (Wstat: 0 Tests: 23 Failed: 3) Failed tests: 5, 7, 12 t/05_vg_find.t (Wstat: 0 Tests: 29 Failed: 1) Failed test: 21 t/07_vg_map.t (Wstat: 0 Tests: 55 Failed: 10) Failed tests: 43-52 t/09_vg_concat.t (Wstat: 0 Tests: 4 Failed: 1) Failed test: 4 t/14_vg_mod.t (Wstat: 0 Tests: 32 Failed: 2) Failed tests: 13, 16 t/15_vg_surject.t (Wstat: 0 Tests: 47 Failed: 11) Failed tests: 7, 13, 19-20, 22-28 t/17_vg_augment.t (Wstat: 0 Tests: 39 Failed: 7) Failed tests: 1-7 t/21_vg_filter.t (Wstat: 0 Tests: 13 Failed: 1) Failed test: 12 t/28_translate.t (Wstat: 0 Tests: 2 Failed: 1) Failed test: 2 t/31_vg_add.t (Wstat: 0 Tests: 12 Failed: 3) Failed tests: 10-12 t/32_vg_snarls.t (Wstat: 0 Tests: 19 Failed: 7) Failed tests: 1-5, 13-14 t/34_vg_pack.t (Wstat: 0 Tests: 20 Failed: 1) Failed test: 18 t/36_vg_annotate.t (Wstat: 0 Tests: 9 Failed: 1) Failed test: 9 t/48_vg_convert.t (Wstat: 0 Tests: 106 Failed: 1) Failed test: 23 t/50_vg_giraffe.t (Wstat: 0 Tests: 50 Failed: 13) Failed tests: 20-29, 48-50 Files=53, Tests=1138, 524 wallclock secs ( 0.61 usr 0.18 sys + 724.32 cusr 211.38 csys = 936.49 CPU) Result: FAIL make[1]: [debian/rules:93: override_dh_auto_test-arch] Error 1 (ignored) make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' dh_install bin/vg usr/bin/ make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_lintian -a 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 dpkg-shlibdeps: warning: cannot find library libhandlegraph.so needed by debian/vg/usr/bin/vg (ELF format: 'elf64-littleaarch64' abi: 'ELF:64:l:arm64:0'; RPATH: '') dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -a debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/vg-1.59.0+ds' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-1), " make[1]: Leaving directory '/build/reproducible-path/vg-1.59.0+ds' dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'vg' in '../vg_1.59.0+ds-0.1_arm64.deb'. dpkg-deb: building package 'vg-dbgsym' in '../vg-dbgsym_1.59.0+ds-0.1_arm64.deb'. dpkg-genbuildinfo --build=any -O../vg_1.59.0+ds-0.1_arm64.buildinfo dpkg-genchanges --build=any -O../vg_1.59.0+ds-0.1_arm64.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 2025-11-27T13:34:51Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Thu, 27 Nov 2025 13:34:52 +0000 | +------------------------------------------------------------------------------+ vg_1.59.0+ds-0.1_arm64.changes: ------------------------------- Format: 1.8 Date: Thu, 21 Nov 2024 00:12:52 +0000 Source: vg Binary: vg vg-dbgsym Architecture: arm64 Version: 1.59.0+ds-0.1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Bastian Germann Description: vg - tools for working with genome variation graphs Closes: 1013061 1043312 1084554 Changes: vg (1.59.0+ds-0.1) unstable; urgency=medium . * Non-maintainer upload . [ Andreas Tille ] * Update lintian override info to new format: + debian/source/lintian-overrides: line 2 + debian/vg.lintian-overrides: line 5, 8-12 * Remove constraints unnecessary since buster (oldstable): + Build-Depends: Replace dependency on transitional package libncurses5-dev with replacement libtinfo6, libncurses-dev. . [ Pierre Gruet ] * Using tags and filenamemangle in d/watch . [ Michael R. Crusoe ] * New upstream version. Closes: #1013061, #1084554 * Added patch to deal with bashim. * debian/rules: unset LD_PRELOAD for qemu build + testing * debian/rules: if the SIMD level is supported by the build CPU as reported by lscpu, then require the tests for that version of the vg binary to pass. * debian/copyright: freshen * Freshen patches * update clean list * Standards-Version: 4.6.2 (routine-update) * Keep vendored copy of libssw until vg updates to a regular release * Refreshed patches, moved some of the crossbuild fixes into earlier patches to reduce churn. * d/patches/series: skip the ssw patches to use the code copy for now. * d/control: new build-dep: libzstd-dev * Force the use of the system package for SIMDe. * Added patch to fix gcc 12+ issues. * d/copyright: exclude the unused benchmarks.js from the vendored copies of atomic_queue * d/control: update names of obsolete packages to their replacements. Closes: #1043312 * Ignore test failures Checksums-Sha1: 4528f405b0dc09056a25a3d8b528b3e809facdff 171125844 vg-dbgsym_1.59.0+ds-0.1_arm64.deb 5a347edaf4c96f2ad8a1893799e1ee76e4be692b 15056 vg_1.59.0+ds-0.1_arm64.buildinfo 70f4de853467627a0d921c6ac04a80706e1b83e8 8049508 vg_1.59.0+ds-0.1_arm64.deb Checksums-Sha256: 91d9024c6eb97bdf20707118d9f9ebc753b028f8758fe5dda03bee95389fc9bd 171125844 vg-dbgsym_1.59.0+ds-0.1_arm64.deb 330677c0ffc42aba60a4e30e2ac6b3ba48d189529376749e161f04a55581c878 15056 vg_1.59.0+ds-0.1_arm64.buildinfo 28d305baed1b3a36e423ba71ee2c8fb8b36ab09d00d0bfbcc6a8c5868035ec1c 8049508 vg_1.59.0+ds-0.1_arm64.deb Files: 78bc684887d86b9131d2d3ac44066592 171125844 debug optional vg-dbgsym_1.59.0+ds-0.1_arm64.deb a38488f3ac0be16f4d4945d0f5062346 15056 science optional vg_1.59.0+ds-0.1_arm64.buildinfo 68a7cb353da768013fa751a8c6b9cb3e 8049508 science optional vg_1.59.0+ds-0.1_arm64.deb +------------------------------------------------------------------------------+ | Buildinfo Thu, 27 Nov 2025 13:34:53 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: vg Binary: vg vg-dbgsym Architecture: arm64 Version: 1.59.0+ds-0.1 Checksums-Md5: 78bc684887d86b9131d2d3ac44066592 171125844 vg-dbgsym_1.59.0+ds-0.1_arm64.deb 68a7cb353da768013fa751a8c6b9cb3e 8049508 vg_1.59.0+ds-0.1_arm64.deb Checksums-Sha1: 4528f405b0dc09056a25a3d8b528b3e809facdff 171125844 vg-dbgsym_1.59.0+ds-0.1_arm64.deb 70f4de853467627a0d921c6ac04a80706e1b83e8 8049508 vg_1.59.0+ds-0.1_arm64.deb Checksums-Sha256: 91d9024c6eb97bdf20707118d9f9ebc753b028f8758fe5dda03bee95389fc9bd 171125844 vg-dbgsym_1.59.0+ds-0.1_arm64.deb 28d305baed1b3a36e423ba71ee2c8fb8b36ab09d00d0bfbcc6a8c5868035ec1c 8049508 vg_1.59.0+ds-0.1_arm64.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Thu, 27 Nov 2025 13:34:49 +0000 Build-Path: /build/reproducible-path/vg-1.59.0+ds Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.5), base-passwd (= 3.6.5), bash (= 5.2.32-1+b2), bc (= 1.07.1-4+b1), binutils (= 2.43.1-5), binutils-aarch64-linux-gnu (= 2.43.1-5), binutils-common (= 2.43.1-5), bison (= 2:3.8.2+dfsg-1+b2), bsdextrautils (= 2.40.2-11), bsdutils (= 1:2.40.2-11), build-essential (= 12.12), bwa (= 0.7.18-1), bzip2 (= 1.0.8-6), ca-certificates (= 20240203), cmake (= 3.31.1-1), cmake-data (= 3.31.1-1), comerr-dev (= 2.1-1.47.1-1+b1), coreutils (= 9.5-1+b1), cpp (= 4:14.2.0-1), cpp-14 (= 14.2.0-8), cpp-14-aarch64-linux-gnu (= 14.2.0-8), cpp-aarch64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-9+b1), debconf (= 1.5.87), debhelper (= 13.20), debianutils (= 5.21), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1+b1), docbook (= 4.5-11), docbook-to-man (= 1:2.0.0-47+b1), docbook-xml (= 4.5-13), docbook-xsl (= 1.79.2+dfsg-7), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), elfutils (= 0.192-4), fastahack (= 1.0.0+dfsg-11+b2), file (= 1:5.45-3+b1), findutils (= 4.10.0-3), flex (= 2.6.4-8.2+b3), fontconfig (= 2.15.0-1.1+b1), fontconfig-config (= 2.15.0-1.1+b1), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-8), g++-14-aarch64-linux-gnu (= 14.2.0-8), g++-aarch64-linux-gnu (= 4:14.2.0-1), gawk (= 1:5.2.1-2+b2), gcc (= 4:14.2.0-1), gcc-14 (= 14.2.0-8), gcc-14-aarch64-linux-gnu (= 14.2.0-8), gcc-14-base (= 14.2.0-8), gcc-aarch64-linux-gnu (= 4:14.2.0-1), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), girepository-tools (= 2.82.2-3), grep (= 3.11-4+b1), groff-base (= 1.23.0-5), gtk-doc-tools (= 1.34.0-1), gzip (= 1.12-1.1+b1), help2man (= 1.49.3+b1), hostname (= 3.25), icu-devtools (= 72.1-5+b1), init-system-helpers (= 1.67), intltool-debian (= 0.35.0+20060710.6), jq (= 1.7.1-3+b1), krb5-multidev (= 1.21.3-3), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.7.4-1.1), libasan8 (= 14.2.0-8), libasm1t64 (= 0.192-4), libatomic1 (= 14.2.0-8), libattr1 (= 1:2.5.2-2), libaudit-common (= 1:4.0.2-2), libaudit1 (= 1:4.0.2-2), libbackward-cpp-dev (= 1.6-1), libbinutils (= 2.43.1-5), libblas3 (= 3.12.0-4), libblkid-dev (= 2.40.2-11), libblkid1 (= 2.40.2-11), libboost-program-options-dev (= 1.83.0.2+b2), libboost-program-options1.83-dev (= 1.83.0-3.2+b1), libboost-program-options1.83.0 (= 1.83.0-3.2+b1), libboost1.83-dev (= 1.83.0-3.2+b1), libbrotli-dev (= 1.1.0-2+b6), libbrotli1 (= 1.1.0-2+b6), libbz2-1.0 (= 1.0.8-6), libbz2-dev (= 1.0.8-6), libc-bin (= 2.40-3), libc-dev-bin (= 2.40-3), libc6 (= 2.40-3), libc6-dev (= 2.40-3), libcairo-gobject2 (= 1.18.2-2), libcairo-script-interpreter2 (= 1.18.2-2), libcairo2 (= 1.18.2-2), libcairo2-dev (= 1.18.2-2), libcap-ng0 (= 0.8.5-3+b1), libcap2 (= 1:2.66-5+b1), libcc1-0 (= 14.2.0-8), libcom-err2 (= 1.47.1-1+b1), libcrypt-dev (= 1:4.4.36-5), libcrypt1 (= 1:4.4.36-5), libctf-nobfd0 (= 2.43.1-5), libctf0 (= 2.43.1-5), libcurl3t64-gnutls (= 8.11.0-1), libcurl4-gnutls-dev (= 8.11.0-1), libcurl4t64 (= 8.11.0-1), libdatrie1 (= 0.2.13-3+b1), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.273), libdebhelper-perl (= 13.20), libdebuginfod-common (= 0.192-4), libdebuginfod1t64 (= 0.192-4), libdeflate-dev (= 1.22-1), libdeflate0 (= 1.22-1), libdisorder-dev (= 0.0.2+git20130809.8062ee1-4+b2), libdisorder0 (= 0.0.2+git20130809.8062ee1-4+b2), libdivsufsort-dev (= 2.0.1-6+b1), libdivsufsort3 (= 2.0.1-6+b1), libdpkg-perl (= 1.22.11), libdw-dev (= 0.192-4), libdw1t64 (= 0.192-4), libelf-dev (= 0.192-4), libelf1t64 (= 0.192-4), libevent-2.1-7t64 (= 2.1.12-stable-10+b1), libexpat1 (= 2.6.4-1), libexpat1-dev (= 2.6.4-1), libfastahack-dev (= 1.0.0+dfsg-11+b2), libfastahack0 (= 1.0.0+dfsg-11+b2), libffi-dev (= 3.4.6-1), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libfml-dev (= 0.1+git20190320.b499514-1+b2), libfml0 (= 0.1+git20190320.b499514-1+b2), libfontconfig-dev (= 2.15.0-1.1+b1), libfontconfig1 (= 2.15.0-1.1+b1), libfreetype-dev (= 2.13.3+dfsg-1), libfreetype6 (= 2.13.3+dfsg-1), libfribidi0 (= 1.0.15-1), libgcc-14-dev (= 14.2.0-8), libgcc-s1 (= 14.2.0-8), libgcrypt20 (= 1.11.0-6), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgfortran5 (= 14.2.0-8), libgio-2.0-dev (= 2.82.2-3), libgio-2.0-dev-bin (= 2.82.2-3), libgirepository-2.0-0 (= 2.82.2-3), libglib2.0-0t64 (= 2.82.2-3), libglib2.0-bin (= 2.82.2-3), libglib2.0-data (= 2.82.2-3), libglib2.0-dev (= 2.82.2-3), libglib2.0-dev-bin (= 2.82.2-3), libgmp-dev (= 2:6.3.0+dfsg-2+b2), libgmp10 (= 2:6.3.0+dfsg-2+b2), libgmpxx4ldbl (= 2:6.3.0+dfsg-2+b2), libgnutls-dane0t64 (= 3.8.8-2), libgnutls-openssl27t64 (= 3.8.8-2), libgnutls28-dev (= 3.8.8-2), libgnutls30t64 (= 3.8.8-2), libgomp1 (= 14.2.0-8), libgpg-error0 (= 1.50-4), libgprofng0 (= 2.43.1-5), libgraphite2-3 (= 1.3.14-2+b1), libgssapi-krb5-2 (= 1.21.3-3), libgssrpc4t64 (= 1.21.3-3), libharfbuzz0b (= 10.0.1-1), libhogweed6t64 (= 3.10-1+b1), libhts-dev (= 1.20+ds-2), libhts3t64 (= 1.20+ds-2), libhtscodecs2 (= 1.6.1-1), libhwasan0 (= 14.2.0-8), libice-dev (= 2:1.1.1-1), libice6 (= 2:1.1.1-1), libicu-dev (= 72.1-5+b1), libicu72 (= 72.1-5+b1), libidn2-0 (= 2.3.7-2+b1), libidn2-dev (= 2.3.7-2+b1), libisl23 (= 0.27-1), libitm1 (= 14.2.0-8), libjansson-dev (= 2.14-2+b3), libjansson4 (= 2.14-2+b3), libjbig0 (= 2.1-6.1+b2), libjemalloc-dev (= 5.3.0-2+b2), libjemalloc2 (= 5.3.0-2+b2), libjpeg62-turbo (= 1:2.1.5-3+b1), libjq1 (= 1.7.1-3+b1), libjson-c5 (= 0.18+ds-1), libjsoncpp26 (= 1.9.6-3), libk5crypto3 (= 1.21.3-3), libkadm5clnt-mit12 (= 1.21.3-3), libkadm5srv-mit12 (= 1.21.3-3), libkdb5-10t64 (= 1.21.3-3), libkeyutils1 (= 1.6.3-4), libkrb5-3 (= 1.21.3-3), libkrb5-dev (= 1.21.3-3), libkrb5support0 (= 1.21.3-3), liblapack3 (= 3.12.0-4), libldap-2.5-0 (= 2.5.18+dfsg-3+b1), libldap-dev (= 2.5.18+dfsg-3+b1), liblerc4 (= 4.0.0+ds-5), liblocale-gettext-perl (= 1.07-7+b1), liblsan0 (= 14.2.0-8), libltdl7 (= 2.4.7-8), liblz4-1 (= 1.9.4-3+b1), liblz4-dev (= 1.9.4-3+b1), liblzma-dev (= 5.6.3-1+b1), liblzma5 (= 5.6.3-1+b1), liblzo2-2 (= 2.10-3+b1), libmagic-mgc (= 1:5.45-3+b1), libmagic1t64 (= 1:5.45-3+b1), libmd0 (= 1.1.0-2+b1), libmhash2 (= 0.9.9.9-10), libmount-dev (= 2.40.2-11), libmount1 (= 2.40.2-11), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.1-1+b2), libncurses-dev (= 6.5-2+b1), libncurses6 (= 6.5-2+b1), libncursesw6 (= 6.5-2+b1), libnettle8t64 (= 3.10-1+b1), libnghttp2-14 (= 1.64.0-1), libnghttp2-dev (= 1.64.0-1), libnghttp3-9 (= 1.4.0-1+b1), libnghttp3-dev (= 1.4.0-1+b1), libngtcp2-16 (= 1.6.0-1), libngtcp2-crypto-gnutls-dev (= 1.6.0-1), libngtcp2-crypto-gnutls8 (= 1.6.0-1), libngtcp2-dev (= 1.6.0-1), libnsl2 (= 1.3.0-3+b3), libonig5 (= 6.9.9-1+b1), libosp5 (= 1.5.2-15+b1), libp11-kit-dev (= 0.25.5-2+b1), libp11-kit0 (= 0.25.5-2+b1), libpam-modules (= 1.5.3-7+b1), libpam-modules-bin (= 1.5.3-7+b1), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7+b1), libpango-1.0-0 (= 1.54.0+ds-3), libpangocairo-1.0-0 (= 1.54.0+ds-3), libpangoft2-1.0-0 (= 1.54.0+ds-3), libpaper-utils (= 1.1.29+b2), libpaper1 (= 1.1.29+b2), libpcre2-16-0 (= 10.44-4), libpcre2-32-0 (= 10.44-4), libpcre2-8-0 (= 10.44-4), libpcre2-dev (= 10.44-4), libpcre2-posix3 (= 10.44-4), libperl5.40 (= 5.40.0-7), libpipeline1 (= 1.5.8-1), libpixman-1-0 (= 0.44.0-3), libpixman-1-dev (= 0.44.0-3), libpkgconf3 (= 1.8.1-4), libpng-dev (= 1.6.44-2), libpng16-16t64 (= 1.6.44-2), libproc2-0 (= 2:4.0.4-6), libprotobuf-dev (= 3.21.12-10+b1), libprotobuf-lite32t64 (= 3.21.12-10+b1), libprotobuf32t64 (= 3.21.12-10+b1), libprotoc-dev (= 3.21.12-10+b1), libprotoc32t64 (= 3.21.12-10+b1), libpsl-dev (= 0.21.2-1.1+b1), libpsl5t64 (= 0.21.2-1.1+b1), libpython3-stdlib (= 3.12.7-1), libpython3.12-minimal (= 3.12.7-3), libpython3.12-stdlib (= 3.12.7-3), libraptor2-0 (= 2.0.16-4+b1), libraptor2-dev (= 2.0.16-4+b1), librasqal3-dev (= 0.9.33-2.1+b2), librasqal3t64 (= 0.9.33-2.1+b2), librdf0-dev (= 1.0.17-4+b1), librdf0t64 (= 1.0.17-4+b1), libreadline8t64 (= 8.2-5), librhash1 (= 1.4.5-1), librtmp-dev (= 2.4+20151223.gitfa8646d.1-2+b5), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5), libsasl2-2 (= 2.1.28+dfsg1-8), libsasl2-modules-db (= 2.1.28+dfsg1-8), libseccomp2 (= 2.5.5-1+b3), libselinux1 (= 3.7-3+b1), libselinux1-dev (= 3.7-3+b1), libsepol-dev (= 3.7-1), libsepol2 (= 3.7-1), libsframe1 (= 2.43.1-5), libsharpyuv0 (= 1.4.0-0.1+b1), libsigsegv2 (= 2.14-1+b2), libsimde-dev (= 0.8.2-1), libsm-dev (= 2:1.2.4-1), libsm6 (= 2:1.2.4-1), libsmartcols1 (= 2.40.2-11), libsmithwaterman-dev (= 0.0+git20160702.2610e25-12+b2), libsmithwaterman0 (= 0.0+git20160702.2610e25-12+b2), libsparsehash-dev (= 2.0.3-2), libsqlite3-0 (= 3.46.1-1), libssh2-1-dev (= 1.11.1-1), libssh2-1t64 (= 1.11.1-1), libssl-dev (= 3.3.2-2), libssl3t64 (= 3.3.2-2), libssw-dev (= 1.1-15+b1), libssw0 (= 1.1-15+b1), libstdc++-14-dev (= 14.2.0-8), libstdc++6 (= 14.2.0-8), libsysprof-capture-4-dev (= 47.1-1), libsystemd0 (= 257~rc2-3), libtabixpp-dev (= 1.1.2-2.1+b1), libtabixpp0t64 (= 1.1.2-2.1+b1), libtasn1-6 (= 4.19.0-3+b3), libtasn1-6-dev (= 4.19.0-3+b3), libtcl8.6 (= 8.6.15+dfsg-2), libthai-data (= 0.1.29-2), libthai0 (= 0.1.29-2+b1), libtiff6 (= 4.5.1+git230720-5), libtinfo6 (= 6.5-2+b1), libtirpc-common (= 1.3.4+ds-1.3), libtirpc3t64 (= 1.3.4+ds-1.3+b1), libtk8.6 (= 8.6.15-1), libtool (= 2.4.7-8), libtsan2 (= 14.2.0-8), libtsl-hopscotch-map-dev (= 2.3.1-1), libubsan1 (= 14.2.0-8), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257~rc2-3), libunbound8 (= 1.22.0-1), libunistring5 (= 1.2-1+b1), libuuid1 (= 2.40.2-11), libuv1t64 (= 1.48.0-7), libvcflib-dev (= 1.0.9+dfsg1-3+b2), libvcflib-tools (= 1.0.9+dfsg1-3+b2), libvcflib2 (= 1.0.9+dfsg1-3+b2), libwebp7 (= 1.4.0-0.1+b1), libwfa2-0 (= 2.3.3-4+b1), libwfa2-dev (= 2.3.3-4+b1), libx11-6 (= 2:1.8.10-2), libx11-data (= 2:1.8.10-2), libx11-dev (= 2:1.8.10-2), libxau-dev (= 1:1.0.11-1), libxau6 (= 1:1.0.11-1), libxcb-render0 (= 1.17.0-2+b1), libxcb-render0-dev (= 1.17.0-2+b1), libxcb-shm0 (= 1.17.0-2+b1), libxcb-shm0-dev (= 1.17.0-2+b1), libxcb1 (= 1.17.0-2+b1), libxcb1-dev (= 1.17.0-2+b1), libxdmcp-dev (= 1:1.1.5-1), libxdmcp6 (= 1:1.1.5-1), libxext-dev (= 2:1.3.4-1+b2), libxext6 (= 2:1.3.4-1+b2), libxft2 (= 2.3.6-1+b2), libxml2 (= 2.12.7+dfsg+really2.9.14-0.2+b1), libxml2-dev (= 2.12.7+dfsg+really2.9.14-0.2+b1), libxrender-dev (= 1:0.9.10-1.1+b2), libxrender1 (= 1:0.9.10-1.1+b2), libxslt1-dev (= 1.1.35-1.1+b1), libxslt1.1 (= 1.1.35-1.1+b1), libxss1 (= 1:1.2.3-1+b2), libxt6t64 (= 1:1.2.1-1.2+b1), libxxhash0 (= 0.8.2-2+b2), libyajl-dev (= 2.1.0-5+b2), libyajl2 (= 2.1.0-5+b2), libzstd-dev (= 1.5.6+dfsg-1+b1), libzstd1 (= 1.5.6+dfsg-1+b1), linux-libc-dev (= 6.11.9-1), littler (= 0.3.20-1), m4 (= 1.4.19-4), make (= 4.3-4.1+b1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), media-types (= 10.1.0), native-architecture (= 0.2.3), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2+b1), netbase (= 6.4), nettle-dev (= 3.10-1+b1), opensp (= 1.5.2-15+b1), openssl (= 3.3.2-2), openssl-provider-legacy (= 3.3.2-2), patch (= 2.7.6-7+b1), perl (= 5.40.0-7), perl-base (= 5.40.0-7), perl-modules-5.40 (= 5.40.0-7), pkgconf (= 1.8.1-4), pkgconf-bin (= 1.8.1-4), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-6), protobuf-compiler (= 3.21.12-10+b1), pv (= 1.9.0-1), python3 (= 3.12.7-1), python3-autocommand (= 2.2.2-3), python3-inflect (= 7.3.1-2), python3-jaraco.context (= 6.0.0-1), python3-jaraco.functools (= 4.1.0-1), python3-lxml (= 5.3.0-1+b1), python3-minimal (= 3.12.7-1), python3-more-itertools (= 10.5.0-1), python3-packaging (= 24.2-1), python3-pkg-resources (= 75.2.0-1), python3-pygments (= 2.18.0+dfsg-1), python3-typeguard (= 4.4.1-1), python3-typing-extensions (= 4.12.2-2), python3.12 (= 3.12.7-3), python3.12-minimal (= 3.12.7-3), r-base-core (= 4.4.2-1), r-cran-cli (= 3.6.3-1), r-cran-colorspace (= 2.1-1+dfsg-1), r-cran-fansi (= 1.0.5-1+b1), r-cran-farver (= 2.1.2-1+b1), r-cran-ggplot2 (= 3.5.1+dfsg-1), r-cran-glue (= 1.7.0-1+b1), r-cran-gridbase (= 0.4-7-5), r-cran-gtable (= 0.3.6+dfsg-1), r-cran-isoband (= 0.2.7-1+b1), r-cran-labeling (= 0.4.3-1), r-cran-lattice (= 0.22-6-1+b1), r-cran-lifecycle (= 1.0.4+dfsg-1), r-cran-littler (= 0.3.20-1+b1), r-cran-magrittr (= 2.0.3-1+b1), r-cran-mass (= 7.3-61-1+b1), r-cran-matrix (= 1.7-1-1), r-cran-mgcv (= 1.9-1-1+b1), r-cran-munsell (= 0.5.1-1), r-cran-nlme (= 3.1.166-1), r-cran-pillar (= 1.9.0+dfsg-1), r-cran-pkgconfig (= 2.0.3-2), r-cran-pkgkitten (= 0.2.4-1), r-cran-plyr (= 1.8.9-1+b1), r-cran-r6 (= 2.5.1-1), r-cran-rcolorbrewer (= 1.1-3-1), r-cran-rcpp (= 1.0.13-1-1), r-cran-rlang (= 1.1.4-1+b1), r-cran-scales (= 1.3.0-1), r-cran-tibble (= 3.2.1+dfsg-2+b1), r-cran-utf8 (= 1.2.4-1+b1), r-cran-vctrs (= 0.6.5-1+b1), r-cran-viridislite (= 0.4.2-2), r-cran-withr (= 3.0.2+dfsg-1), rapidjson-dev (= 1.1.0+dfsg2-7.3), raptor2-utils (= 2.0.16-4+b1), rasqal-utils (= 0.9.33-2.1+b2), readline-common (= 8.2-5), rpcsvc-proto (= 1.4.3-1+b1), rs (= 20200313-1+b1), samtools (= 1.20-3+b1), sed (= 4.9-2+b1), sensible-utils (= 0.0.24), sgml-base (= 1.31), sgml-data (= 2.0.11+nmu1), sysvinit-utils (= 3.11-1), tabix (= 1.20+ds-2), tar (= 1.35+dfsg-3+b1), tzdata (= 2024b-3), ucf (= 3.0043+nmu1), unzip (= 6.0-28+b1), usr-is-merged (= 39), util-linux (= 2.40.2-11), uuid-dev (= 2.40.2-11), x11-common (= 1:7.7+23.1), x11proto-core-dev (= 2024.1-1), x11proto-dev (= 2024.1-1), xdg-utils (= 1.1.3-4.1), xml-core (= 0.19), xorg-sgml-doctools (= 1:1.11-1.1), xsltproc (= 1.1.35-1.1+b1), xtrans-dev (= 1.4.0-1), xxd (= 2:9.1.0861-1), xz-utils (= 5.6.3-1+b1), zip (= 3.0-14+b1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1732147972" +------------------------------------------------------------------------------+ | Package contents Thu, 27 Nov 2025 13:34:53 +0000 | +------------------------------------------------------------------------------+ vg-dbgsym_1.59.0+ds-0.1_arm64.deb --------------------------------- new Debian package, version 2.0. size 171125844 bytes: control archive=536 bytes. 365 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: vg-dbgsym Source: vg Version: 1.59.0+ds-0.1 Auto-Built-Package: debug-symbols Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 172621 Depends: vg (= 1.59.0+ds-0.1) Section: debug Priority: optional Description: debug symbols for vg Build-Ids: f2b8b46bf57b2ab54196b62062c089b7ca3f5463 drwxr-xr-x root/root 0 2024-11-21 00:12 ./ drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/ drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/lib/ drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/lib/debug/.build-id/f2/ -rw-r--r-- root/root 176753472 2024-11-21 00:12 ./usr/lib/debug/.build-id/f2/b8b46bf57b2ab54196b62062c089b7ca3f5463.debug drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/share/ drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-11-21 00:12 ./usr/share/doc/vg-dbgsym -> vg vg_1.59.0+ds-0.1_arm64.deb -------------------------- new Debian package, version 2.0. size 8049508 bytes: control archive=1268 bytes. 1513 bytes, 27 lines control 303 bytes, 5 lines md5sums Package: vg Version: 1.59.0+ds-0.1 Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 29903 Depends: libatomic1 (>= 4.8), libc6 (>= 2.38), libcairo2 (>= 1.2.4), libdivsufsort3 (>= 2.0.1), libfastahack0 (>= 0.0+git20160702.bbc645f), libgcc-s1 (>= 3.0), libgomp1 (>= 9), libhts3t64 (>= 1.17), libraptor2-0 (>= 2.0.15), libstdc++6 (>= 14), libtabixpp0t64 (>= 1.0.0), libvcflib2 (>= 1.0.9+dfsg1), libzstd1 (>= 1.5.5), zlib1g (>= 1:1.2.0.2) Conflicts: cgvg Built-Using: simde (= 0.8.2-1) Section: science Priority: optional Homepage: https://github.com/vgteam/vg#vg Description: tools for working with genome variation graphs variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods . Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: . - nodes, which are labeled by sequences and ids - edges, which connect two nodes via either of their respective ends - paths, describe genomes, sequence alignments, and annotations (such as gene models and transcripts) as walks through nodes connected by edges . This model is similar to a number of sequence graphs that have been used in assembly and multiple sequence alignment. Paths provide coordinate systems relative to genomes encoded in the graph, allowing stable mappings to be produced even if the structure of the graph is changed. drwxr-xr-x root/root 0 2024-11-21 00:12 ./ drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/ drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/bin/ -rwxr-xr-x root/root 30585824 2024-11-21 00:12 ./usr/bin/vg drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/share/ drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/share/doc/vg/ -rw-r--r-- root/root 2354 2024-11-21 00:12 ./usr/share/doc/vg/changelog.Debian.gz -rw-r--r-- root/root 18307 2024-11-21 00:12 ./usr/share/doc/vg/copyright drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 649 2024-11-21 00:12 ./usr/share/lintian/overrides/vg drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/share/man/ drwxr-xr-x root/root 0 2024-11-21 00:12 ./usr/share/man/man1/ -rw-r--r-- root/root 262 2024-11-21 00:12 ./usr/share/man/man1/vg.1.gz +------------------------------------------------------------------------------+ | Post Build Thu, 27 Nov 2025 13:34:57 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Thu, 27 Nov 2025 13:34:57 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Thu, 27 Nov 2025 13:35:00 +0000 | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: 4740740 Build-Time: 1606 Distribution: unstable Host Architecture: arm64 Install-Time: 6 Job: /srv/rebuilderd/tmp/rebuilderd6UeE2X/inputs/vg_1.59.0+ds-0.1.dsc Machine Architecture: arm64 Package: vg Package-Time: 1634 Source-Version: 1.59.0+ds-0.1 Space: 4740740 Status: successful Version: 1.59.0+ds-0.1 -------------------------------------------------------------------------------- Finished at 2025-11-27T13:34:51Z Build needed 00:27:14, 4740740k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderd6UeE2X/out checking vg-dbgsym_1.59.0+ds-0.1_arm64.deb: size differs for vg-dbgsym_1.59.0+ds-0.1_arm64.deb