=============================================================================== 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/rebuilderdR7kwFT/inputs/sga_0.10.15-7+b1_armel.buildinfo Source: sga Version: 0.10.15-7 rebuilderd-worker node: codethink05-arm64 +------------------------------------------------------------------------------+ | Downloading sources Mon, 28 Jul 2025 22:55:45 +0000 | +------------------------------------------------------------------------------+ Get:1 https://deb.debian.org/debian trixie InRelease [168 kB] Get:2 https://deb.debian.org/debian sid InRelease [213 kB] Get:3 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:4 https://deb.debian.org/debian sid/main Sources [11.0 MB] Fetched 21.9 MB in 2s (10.7 MB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/s/sga/sga_0.10.15-7.dsc' sga_0.10.15-7.dsc 2084 SHA256:b3ec2546141c8a35c7726788237794b3de9ceb57a89f5b58fe94713ddf63afbd 'https://deb.debian.org/debian/pool/main/s/sga/sga_0.10.15.orig.tar.gz' sga_0.10.15.orig.tar.gz 6569986 SHA256:1b18996e6ec47985bc4889a8cbc3cd4dd3a8c7d385ae9f450bd474e36342558b 'https://deb.debian.org/debian/pool/main/s/sga/sga_0.10.15-7.debian.tar.xz' sga_0.10.15-7.debian.tar.xz 214356 SHA256:708c923249099329004802eb6fe1b549b6421e5d3cf10d81c624db65e381117f 1b18996e6ec47985bc4889a8cbc3cd4dd3a8c7d385ae9f450bd474e36342558b sga_0.10.15.orig.tar.gz 708c923249099329004802eb6fe1b549b6421e5d3cf10d81c624db65e381117f sga_0.10.15-7.debian.tar.xz b3ec2546141c8a35c7726788237794b3de9ceb57a89f5b58fe94713ddf63afbd sga_0.10.15-7.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Mon, 28 Jul 2025 22:55:47 +0000 | +------------------------------------------------------------------------------+ Rebuilding sga=0.10.15-7 in /srv/rebuilderd/tmp/rebuilderdR7kwFT/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdR7kwFT/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdR7kwFT/inputs/sga_0.10.15-7+b1_armel.buildinfo /srv/rebuilderd/tmp/rebuilderdR7kwFT/inputs/sga_0.10.15-7+b1_armel.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/sga-qoWx2H/sga-0.10.15 I: verifying dsc... successful! Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm InRelease [157 kB] Get:2 http://snapshot.debian.org/archive/debian/20220921T235202Z bookworm InRelease [161 kB] Get:3 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel Packages [8112 kB] Get:4 http://snapshot.debian.org/archive/debian/20220921T235202Z bookworm/main armel Packages [8135 kB] Fetched 16.6 MB in 2s (9969 kB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20220903T155935Z/dists/bookworm/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted W: http://snapshot.debian.org/archive/debian/20220921T235202Z/dists/bookworm/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel bzip2 armel 1.0.8-5 [49.9 kB] Fetched 49.9 kB in 0s (2764 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4nth52po/bzip2_1.0.8-5_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libkeyutils1 armel 1.6.3-1 [14.8 kB] Fetched 14.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjakijc97/libkeyutils1_1.6.3-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel gcc-12-base armel 12.2.0-1 [208 kB] Fetched 208 kB in 0s (10.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0ad3v7bq/gcc-12-base_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel util-linux-extra armel 2.38.1-1 [158 kB] Fetched 158 kB in 0s (7767 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpson484bc/util-linux-extra_2.38.1-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libkrb5support0 armel 1.20-1 [62.6 kB] Fetched 62.6 kB in 0s (3105 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphkwrkspu/libkrb5support0_1.20-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libp11-kit0 armel 0.24.1-1 [328 kB] Fetched 328 kB in 0s (18.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3w16ynbd/libp11-kit0_0.24.1-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel g++-12 armel 12.2.0-1 [7917 kB] Fetched 7917 kB in 0s (106 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx8oylcqr/g++-12_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libdebhelper-perl all 13.9.1 [196 kB] Fetched 196 kB in 0s (14.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt7gai3o3/libdebhelper-perl_13.9.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel cpp-12 armel 12.2.0-1 [7161 kB] Fetched 7161 kB in 0s (130 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc8bbtkxn/cpp-12_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libdeflate0 armel 1.12-1 [52.8 kB] Fetched 52.8 kB in 0s (4584 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppnbe8lv7/libdeflate0_1.12-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel login armel 1:4.11.1+dfsg1-2 [612 kB] Fetched 612 kB in 0s (27.0 MB/s) dpkg-name: info: moved 'login_1%3a4.11.1+dfsg1-2_armel.deb' to '/srv/rebuilderd/tmp/tmpi15we4sm/login_4.11.1+dfsg1-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel rpcsvc-proto armel 1.4.2-4 [58.4 kB] Fetched 58.4 kB in 0s (3643 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9jzoxxm1/rpcsvc-proto_1.4.2-4_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpam0g armel 1.5.2-2 [127 kB] Fetched 127 kB in 0s (10.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsoxgs356/libpam0g_1.5.2-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel python3.10-minimal armel 3.10.6-1 [1618 kB] Fetched 1618 kB in 0s (52.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9n6odgej/python3.10-minimal_3.10.6-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220921T235202Z bookworm/main armel libglib2.0-0 armel 2.73.3-3 [1269 kB] Fetched 1269 kB in 0s (63.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp38llp7jl/libglib2.0-0_2.73.3-3_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libstdc++6 armel 12.2.0-1 [507 kB] Fetched 507 kB in 0s (22.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprsuxezk3/libstdc++6_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel man-db armel 2.10.2-2 [1372 kB] Fetched 1372 kB in 0s (52.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2x5o9ztn/man-db_2.10.2-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libnsl2 armel 1.3.0-2 [33.0 kB] Fetched 33.0 kB in 0s (2608 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn4eb6ukg/libnsl2_1.3.0-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libxcb-shm0 armel 1.15-1 [106 kB] Fetched 106 kB in 0s (6642 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp16mlrhr_/libxcb-shm0_1.15-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libxdmcp6 armel 1:1.1.2-3 [25.0 kB] Fetched 25.0 kB in 0s (2425 kB/s) dpkg-name: info: moved 'libxdmcp6_1%3a1.1.2-3_armel.deb' to '/srv/rebuilderd/tmp/tmp5c7xisre/libxdmcp6_1.1.2-3_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel binutils-common armel 2.38.90.20220713-2 [2313 kB] Fetched 2313 kB in 0s (132 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw6tfw0wg/binutils-common_2.38.90.20220713-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel util-linux armel 2.38.1-1 [1133 kB] Fetched 1133 kB in 0s (37.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptyfj5jtb/util-linux_2.38.1-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libcc1-0 armel 12.2.0-1 [32.2 kB] Fetched 32.2 kB in 0s (1556 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbwi0bc79/libcc1-0_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libssh2-1 armel 1.10.0-3+b1 [161 kB] Fetched 161 kB in 0s (8363 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4bgfgyt2/libssh2-1_1.10.0-3+b1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220921T235202Z bookworm/main armel autopoint all 0.21-9 [510 kB] Fetched 510 kB in 0s (28.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp18ggo1c_/autopoint_0.21-9_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libffi8 armel 3.4.2-4 [21.1 kB] Fetched 21.1 kB in 0s (1532 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptfksz_77/libffi8_3.4.2-4_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libaudit-common all 1:3.0.7-1 [16.0 kB] Fetched 16.0 kB in 0s (966 kB/s) dpkg-name: info: moved 'libaudit-common_1%3a3.0.7-1_all.deb' to '/srv/rebuilderd/tmp/tmpuvoz17rc/libaudit-common_3.0.7-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libcryptsetup12 armel 2:2.5.0-2 [227 kB] Fetched 227 kB in 0s (11.7 MB/s) dpkg-name: info: moved 'libcryptsetup12_2%3a2.5.0-2_armel.deb' to '/srv/rebuilderd/tmp/tmp8pea9p9r/libcryptsetup12_2.5.0-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpangoft2-1.0-0 armel 1.50.9+ds-1 [70.6 kB] Fetched 70.6 kB in 0s (6720 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi47p5crp/libpangoft2-1.0-0_1.50.9+ds-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel xz-utils armel 5.2.5-2.1 [220 kB] Fetched 220 kB in 0s (18.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzwhqmj1x/xz-utils_5.2.5-2.1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libharfbuzz0b armel 2.7.4-1+b1 [1431 kB] Fetched 1431 kB in 0s (64.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvtoyjzgk/libharfbuzz0b_2.7.4-1+b1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libcom-err2 armel 1.46.5-2 [74.9 kB] Fetched 74.9 kB in 0s (5545 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpujh852sc/libcom-err2_1.46.5-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel dash armel 0.5.11+git20210903+057cd650a4ed-8 [107 kB] Fetched 107 kB in 0s (5676 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyr8dxhvc/dash_0.5.11+git20210903+057cd650a4ed-8_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libmagic1 armel 1:5.41-4 [121 kB] Fetched 121 kB in 0s (12.0 MB/s) dpkg-name: info: moved 'libmagic1_1%3a5.41-4_armel.deb' to '/srv/rebuilderd/tmp/tmpwsfivjr_/libmagic1_5.41-4_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libbrotli1 armel 1.0.9-2+b4 [278 kB] Fetched 278 kB in 0s (15.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_nklpcza/libbrotli1_1.0.9-2+b4_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libselinux1 armel 3.4-1+b1 [84.8 kB] Fetched 84.8 kB in 0s (6096 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo6q5_pia/libselinux1_3.4-1+b1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libasan8 armel 12.2.0-1 [2094 kB] Fetched 2094 kB in 0s (90.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpny3hb4da/libasan8_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel samtools armel 1.13-4 [540 kB] Fetched 540 kB in 0s (25.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphh30bvi9/samtools_1.13-4_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpython3.10-minimal armel 3.10.6-1 [812 kB] Fetched 812 kB in 0s (32.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpke3thrqi/libpython3.10-minimal_3.10.6-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel autoconf all 2.71-2 [343 kB] Fetched 343 kB in 0s (16.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzzq934lm/autoconf_2.71-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libcairo2 armel 1.16.0-6 [512 kB] Fetched 512 kB in 0s (23.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnb9uktzt/libcairo2_1.16.0-6_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libkmod2 armel 30+20220630-3 [51.9 kB] Fetched 51.9 kB in 0s (4030 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg42urjlx/libkmod2_30+20220630-3_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libsystemd0 armel 251.4-3 [377 kB] Fetched 377 kB in 0s (18.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprqlx3uoa/libsystemd0_251.4-3_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel x11-common all 1:7.7+23 [252 kB] Fetched 252 kB in 0s (12.9 MB/s) dpkg-name: info: moved 'x11-common_1%3a7.7+23_all.deb' to '/srv/rebuilderd/tmp/tmp5vadgdh7/x11-common_7.7+23_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel diffutils armel 1:3.8-1 [368 kB] Fetched 368 kB in 0s (16.8 MB/s) dpkg-name: info: moved 'diffutils_1%3a3.8-1_armel.deb' to '/srv/rebuilderd/tmp/tmptq90jhdv/diffutils_3.8-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libbinutils armel 2.38.90.20220713-2 [411 kB] Fetched 411 kB in 0s (23.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2_m57t79/libbinutils_2.38.90.20220713-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel python3-ruffus all 2.8.4-4 [152 kB] Fetched 152 kB in 0s (9674 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp948zrbyl/python3-ruffus_2.8.4-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libfreetype6 armel 2.12.1+dfsg-3 [356 kB] Fetched 356 kB in 0s (29.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9lgrl0og/libfreetype6_2.12.1+dfsg-3_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libgcc-s1 armel 12.2.0-1 [38.4 kB] Fetched 38.4 kB in 0s (1889 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptxe4ezfb/libgcc-s1_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libctf-nobfd0 armel 2.38.90.20220713-2 [140 kB] Fetched 140 kB in 0s (7281 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9jxwlwwd/libctf-nobfd0_2.38.90.20220713-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libxaw7 armel 2:1.0.14-1 [167 kB] Fetched 167 kB in 0s (7340 kB/s) dpkg-name: info: moved 'libxaw7_2%3a1.0.14-1_armel.deb' to '/srv/rebuilderd/tmp/tmps3iz5qyk/libxaw7_1.0.14-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel bsdutils armel 1:2.38.1-1 [144 kB] Fetched 144 kB in 0s (7203 kB/s) dpkg-name: info: moved 'bsdutils_1%3a2.38.1-1_armel.deb' to '/srv/rebuilderd/tmp/tmpfwfugd77/bsdutils_2.38.1-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libxmu6 armel 2:1.1.3-3 [53.2 kB] Fetched 53.2 kB in 0s (3502 kB/s) dpkg-name: info: moved 'libxmu6_2%3a1.1.3-3_armel.deb' to '/srv/rebuilderd/tmp/tmpf7wmeflg/libxmu6_1.1.3-3_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libmagic-mgc armel 1:5.41-4 [295 kB] Fetched 295 kB in 0s (21.8 MB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.41-4_armel.deb' to '/srv/rebuilderd/tmp/tmpawpw_edi/libmagic-mgc_5.41-4_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libblkid1 armel 2.38.1-1 [191 kB] Fetched 191 kB in 0s (14.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnqfz88e0/libblkid1_2.38.1-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (5869 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2st2g7g8/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libkrb5-3 armel 1.20-1 [316 kB] Fetched 316 kB in 0s (16.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1bojdwwp/libkrb5-3_1.20-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libk5crypto3 armel 1.20-1 [106 kB] Fetched 106 kB in 0s (6262 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo9m9_n3w/libk5crypto3_1.20-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220921T235202Z bookworm/main armel libcurl3-gnutls armel 7.85.0-1 [320 kB] Fetched 320 kB in 0s (16.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8e1r8ryp/libcurl3-gnutls_7.85.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libgcrypt20 armel 1.10.1-2 [626 kB] Fetched 626 kB in 0s (27.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdi14qe9p/libgcrypt20_1.10.1-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpathplan4 armel 2.42.2-7 [66.0 kB] Fetched 66.0 kB in 0s (5489 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgig5fskx/libpathplan4_2.42.2-7_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel intltool-debian all 0.35.0+20060710.5 [26.8 kB] Fetched 26.8 kB in 0s (1716 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpze9wgjfh/intltool-debian_0.35.0+20060710.5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220921T235202Z bookworm/main armel bash armel 5.2~rc2-2 [1447 kB] Fetched 1447 kB in 0s (50.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4fr08fa_/bash_5.2~rc2-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libhts3 armel 1.13+ds-2+b1 [343 kB] Fetched 343 kB in 0s (9856 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps0ll8w_5/libhts3_1.13+ds-2+b1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libcrypt-dev armel 1:4.4.28-2 [127 kB] Fetched 127 kB in 0s (7484 kB/s) dpkg-name: info: moved 'libcrypt-dev_1%3a4.4.28-2_armel.deb' to '/srv/rebuilderd/tmp/tmprok8obff/libcrypt-dev_4.4.28-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel perl-modules-5.34 all 5.34.0-5 [2850 kB] Fetched 2850 kB in 0s (84.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaeilaput/perl-modules-5.34_5.34.0-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libaudit1 armel 1:3.0.7-1+b1 [49.3 kB] Fetched 49.3 kB in 0s (926 kB/s) dpkg-name: info: moved 'libaudit1_1%3a3.0.7-1+b1_armel.deb' to '/srv/rebuilderd/tmp/tmpzormhosr/libaudit1_3.0.7-1+b1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libmd0 armel 1.0.4-2 [28.9 kB] Fetched 28.9 kB in 0s (2876 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu52lhqei/libmd0_1.0.4-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libsqlite3-0 armel 3.39.2-1 [729 kB] Fetched 729 kB in 0s (40.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprpo58dcu/libsqlite3-0_3.39.2-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libgmp10 armel 2:6.2.1+dfsg1-1 [508 kB] Fetched 508 kB in 0s (22.3 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.2.1+dfsg1-1_armel.deb' to '/srv/rebuilderd/tmp/tmp0qymlk45/libgmp10_6.2.1+dfsg1-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libelf1 armel 0.187-1 [175 kB] Fetched 175 kB in 0s (8476 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsobnxvdg/libelf1_0.187-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel liblerc4 armel 4.0.0+ds-1 [157 kB] Fetched 157 kB in 0s (10.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpelknrrec/liblerc4_4.0.0+ds-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel hostname armel 3.23 [14.2 kB] Fetched 14.2 kB in 0s (823 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxkheragf/hostname_3.23_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel mount armel 2.38.1-1 [184 kB] Fetched 184 kB in 0s (13.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp33msx6i9/mount_2.38.1-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel file armel 1:5.41-4 [66.2 kB] Fetched 66.2 kB in 0s (6495 kB/s) dpkg-name: info: moved 'file_1%3a5.41-4_armel.deb' to '/srv/rebuilderd/tmp/tmpthc667da/file_5.41-4_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libudev1 armel 251.4-3 [176 kB] Fetched 176 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg85tz1zf/libudev1_251.4-3_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel dpkg-dev all 1.21.9 [2361 kB] Fetched 2361 kB in 0s (62.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp84oj59kq/dpkg-dev_1.21.9_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel fontconfig armel 2.13.1-4.4 [416 kB] Fetched 416 kB in 0s (26.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk84gpq88/fontconfig_2.13.1-4.4_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpng16-16 armel 1.6.37-5 [275 kB] Fetched 275 kB in 0s (5262 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl2ykvfbe/libpng16-16_1.6.37-5_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libx11-6 armel 2:1.8.1-2 [705 kB] Fetched 705 kB in 0s (42.5 MB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.1-2_armel.deb' to '/srv/rebuilderd/tmp/tmpm26h_41_/libx11-6_1.8.1-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel sed armel 4.8-1 [309 kB] Fetched 309 kB in 0s (22.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdx7oy3kl/sed_4.8-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libc-bin armel 2.34-7 [777 kB] Fetched 777 kB in 0s (34.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpducg_bd0/libc-bin_2.34-7_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libdb5.3 armel 5.3.28+dfsg1-0.10 [572 kB] Fetched 572 kB in 0s (36.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp__lhwi4n/libdb5.3_5.3.28+dfsg1-0.10_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel liblz4-1 armel 1.9.4-1 [58.1 kB] Fetched 58.1 kB in 0s (3746 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf4i2zkfl/liblz4-1_1.9.4-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libmpdec3 armel 2.5.1-2 [74.6 kB] Fetched 74.6 kB in 0s (5410 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdlfgfsuz/libmpdec3_2.5.1-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel zlib1g armel 1:1.2.11.dfsg-4.1 [84.3 kB] Fetched 84.3 kB in 0s (6713 kB/s) dpkg-name: info: moved 'zlib1g_1%3a1.2.11.dfsg-4.1_armel.deb' to '/srv/rebuilderd/tmp/tmpi35nhrwk/zlib1g_1.2.11.dfsg-4.1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel base-passwd armel 3.6.0 [58.4 kB] Fetched 58.4 kB in 0s (3070 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp97zzu9ne/base-passwd_3.6.0_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel grep armel 3.7-1 [394 kB] Fetched 394 kB in 0s (17.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm47nis32/grep_3.7-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libfribidi0 armel 1.0.8-2.1 [63.6 kB] Fetched 63.6 kB in 0s (3276 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpps71wrab/libfribidi0_1.0.8-2.1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libxpm4 armel 1:3.5.12-1 [43.3 kB] Fetched 43.3 kB in 0s (2119 kB/s) dpkg-name: info: moved 'libxpm4_1%3a3.5.12-1_armel.deb' to '/srv/rebuilderd/tmp/tmp4mtn7f1i/libxpm4_3.5.12-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel binutils-arm-linux-gnueabi armel 2.38.90.20220713-2 [2613 kB] Fetched 2613 kB in 0s (118 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7wnbrgwo/binutils-arm-linux-gnueabi_2.38.90.20220713-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libxcb1 armel 1.15-1 [140 kB] Fetched 140 kB in 0s (7009 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpndgb9a0o/libxcb1_1.15-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel readline-common all 8.2~rc2-2 [75.8 kB] Fetched 75.8 kB in 0s (6509 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphb5y80lk/readline-common_8.2~rc2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libsub-override-perl all 0.09-3 [10.4 kB] Fetched 10.4 kB in 0s (936 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1cdv72yx/libsub-override-perl_0.09-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libmpc3 armel 1.2.1-2 [36.0 kB] Fetched 36.0 kB in 0s (2649 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqk43btpn/libmpc3_1.2.1-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libgraphite2-3 armel 1.3.14-1 [71.4 kB] Fetched 71.4 kB in 0s (6562 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaui4_m3v/libgraphite2-3_1.3.14-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libbsd0 armel 0.11.6-1 [109 kB] Fetched 109 kB in 0s (7521 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgty87y32/libbsd0_0.11.6-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel perl armel 5.34.0-5 [298 kB] Fetched 298 kB in 0s (21.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk0zgogox/perl_5.34.0-5_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libcap2 armel 1:2.44-1 [21.1 kB] Fetched 21.1 kB in 0s (1664 kB/s) dpkg-name: info: moved 'libcap2_1%3a2.44-1_armel.deb' to '/srv/rebuilderd/tmp/tmpppnozdxx/libcap2_2.44-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libapparmor1 armel 3.0.7-1 [99.6 kB] Fetched 99.6 kB in 0s (4860 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgap786fi/libapparmor1_3.0.7-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libuchardet0 armel 0.0.7-1 [65.1 kB] Fetched 65.1 kB in 0s (3389 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkxe5f5ku/libuchardet0_0.0.7-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel dh-autoreconf all 20 [17.1 kB] Fetched 17.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq808oqjw/dh-autoreconf_20_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel dwz armel 0.14-1 [92.5 kB] Fetched 92.5 kB in 0s (7861 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbzhgmpnm/dwz_0.14-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpython3.10-stdlib armel 3.10.6-1 [1604 kB] Fetched 1604 kB in 0s (51.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp84qelhto/libpython3.10-stdlib_3.10.6-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libgd3 armel 2.3.3-6 [121 kB] Fetched 121 kB in 0s (9716 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpntgo2nco/libgd3_2.3.3-6_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libisl23 armel 0.25-1 [517 kB] Fetched 517 kB in 0s (19.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1maef3vo/libisl23_0.25-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel ucf all 3.0043 [74.0 kB] Fetched 74.0 kB in 0s (5191 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7zsh3i8t/ucf_3.0043_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libgdbm6 armel 1.23-1+b1 [78.9 kB] Fetched 78.9 kB in 0s (4549 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyjpe66yh/libgdbm6_1.23-1+b1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel liblocale-gettext-perl armel 1.07-4+b2 [18.3 kB] Fetched 18.3 kB in 0s (1586 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd0us9u4l/liblocale-gettext-perl_1.07-4+b2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel linux-libc-dev armel 5.18.16-1 [1580 kB] Fetched 1580 kB in 0s (66.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf3igieuq/linux-libc-dev_5.18.16-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel findutils armel 4.9.0-3 [662 kB] Fetched 662 kB in 0s (35.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpext82d56/findutils_4.9.0-3_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel mawk armel 1.3.4.20200120-3.1 [110 kB] Fetched 110 kB in 0s (7988 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpktvzvi5e/mawk_1.3.4.20200120-3.1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel autotools-dev all 20220109.1 [51.6 kB] Fetched 51.6 kB in 0s (3379 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp88ldwrik/autotools-dev_20220109.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel gcc-12 armel 12.2.0-1 [14.2 MB] Fetched 14.2 MB in 0s (174 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzjwucbwi/gcc-12_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel ncurses-base all 6.3+20220423-2 [282 kB] Fetched 282 kB in 0s (15.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfyg59isz/ncurses-base_6.3+20220423-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libthai0 armel 0.1.29-1 [54.4 kB] Fetched 54.4 kB in 0s (2900 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptofchuhv/libthai0_0.1.29-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libmpfr6 armel 4.1.0-3 [805 kB] Fetched 805 kB in 0s (34.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9iq86qkx/libmpfr6_4.1.0-3_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel tar armel 1.34+dfsg-1 [816 kB] Fetched 816 kB in 0s (37.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjg03fpx0/tar_1.34+dfsg-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpsl5 armel 0.21.0-1.2 [56.2 kB] Fetched 56.2 kB in 0s (3433 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9nu1ak8o/libpsl5_0.21.0-1.2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libc-dev-bin armel 2.34-7 [246 kB] Fetched 246 kB in 0s (6496 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph_pluv4l/libc-dev-bin_2.34-7_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel liblzma5 armel 5.2.5-2.1 [159 kB] Fetched 159 kB in 0s (1001 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp231r58p1/liblzma5_5.2.5-2.1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel make armel 4.3-4.1 [384 kB] Fetched 384 kB in 0s (22.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpob2qi96d/make_4.3-4.1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libxrender1 armel 1:0.9.10-1.1 [31.3 kB] Fetched 31.3 kB in 0s (2353 kB/s) dpkg-name: info: moved 'libxrender1_1%3a0.9.10-1.1_armel.deb' to '/srv/rebuilderd/tmp/tmpjfy6lwit/libxrender1_0.9.10-1.1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220921T235202Z bookworm/main armel libbamtools2.5.2 armel 2.5.2+dfsg-2 [127 kB] Fetched 127 kB in 0s (1728 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_2hwc1x7/libbamtools2.5.2_2.5.2+dfsg-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libmount1 armel 2.38.1-1 [203 kB] Fetched 203 kB in 0s (16.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl05xblej/libmount1_2.38.1-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel python3-distutils all 3.10.6-1 [141 kB] Fetched 141 kB in 0s (8070 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppe4zhan0/python3-distutils_3.10.6-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel python3-lib2to3 all 3.10.6-1 [79.9 kB] Fetched 79.9 kB in 0s (3917 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplfsyvz0f/python3-lib2to3_3.10.6-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libsystemd-shared armel 251.4-3 [1522 kB] Fetched 1522 kB in 0s (49.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk81ruiov/libsystemd-shared_251.4-3_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel bsdextrautils armel 2.38.1-1 [138 kB] Fetched 138 kB in 0s (6872 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6g40crm_/bsdextrautils_2.38.1-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libattr1 armel 1:2.5.1-1 [20.5 kB] Fetched 20.5 kB in 0s (2026 kB/s) dpkg-name: info: moved 'libattr1_1%3a2.5.1-1_armel.deb' to '/srv/rebuilderd/tmp/tmpelvx9gx_/libattr1_2.5.1-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpango-1.0-0 armel 1.50.9+ds-1 [217 kB] Fetched 217 kB in 0s (13.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3sfy_0o_/libpango-1.0-0_1.50.9+ds-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel fontconfig-config all 2.13.1-4.4 [281 kB] Fetched 281 kB in 0s (23.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzbtcv3x9/fontconfig-config_2.13.1-4.4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libxt6 armel 1:1.2.1-1 [159 kB] Fetched 159 kB in 0s (12.0 MB/s) dpkg-name: info: moved 'libxt6_1%3a1.2.1-1_armel.deb' to '/srv/rebuilderd/tmp/tmp9chz22k6/libxt6_1.2.1-1_armel.deb' Downloading dependency 1 of 255: bzip2:armel=1.0.8-5 Downloading dependency 2 of 255: libkeyutils1:armel=1.6.3-1 Downloading dependency 3 of 255: gcc-12-base:armel=12.2.0-1 Downloading dependency 4 of 255: util-linux-extra:armel=2.38.1-1 Downloading dependency 5 of 255: libkrb5support0:armel=1.20-1 Downloading dependency 6 of 255: libp11-kit0:armel=0.24.1-1 Downloading dependency 7 of 255: g++-12:armel=12.2.0-1 Downloading dependency 8 of 255: libdebhelper-perl:armel=13.9.1 Downloading dependency 9 of 255: cpp-12:armel=12.2.0-1 Downloading dependency 10 of 255: libdeflate0:armel=1.12-1 Downloading dependency 11 of 255: login:armel=1:4.11.1+dfsg1-2 Downloading dependency 12 of 255: rpcsvc-proto:armel=1.4.2-4 Downloading dependency 13 of 255: libpam0g:armel=1.5.2-2 Downloading dependency 14 of 255: python3.10-minimal:armel=3.10.6-1 Downloading dependency 15 of 255: libglib2.0-0:armel=2.73.3-3 Downloading dependency 16 of 255: libstdc++6:armel=12.2.0-1 Downloading dependency 17 of 255: man-db:armel=2.10.2-2 Downloading dependency 18 of 255: libnsl2:armel=1.3.0-2 Downloading dependency 19 of 255: libxcb-shm0:armel=1.15-1 Downloading dependency 20 of 255: libxdmcp6:armel=1:1.1.2-3 Downloading dependency 21 of 255: binutils-common:armel=2.38.90.20220713-2 Downloading dependency 22 of 255: util-linux:armel=2.38.1-1 Downloading dependency 23 of 255: libcc1-0:armel=12.2.0-1 Downloading dependency 24 of 255: libssh2-1:armel=1.10.0-3+b1 Downloading dependency 25 of 255: autopoint:armel=0.21-9 Downloading dependency 26 of 255: libffi8:armel=3.4.2-4 Downloading dependency 27 of 255: libaudit-common:armel=1:3.0.7-1 Downloading dependency 28 of 255: libcryptsetup12:armel=2:2.5.0-2 Downloading dependency 29 of 255: libpangoft2-1.0-0:armel=1.50.9+ds-1 Downloading dependency 30 of 255: xz-utils:armel=5.2.5-2.1 Downloading dependency 31 of 255: libharfbuzz0b:armel=2.7.4-1+b1 Downloading dependency 32 of 255: libcom-err2:armel=1.46.5-2 Downloading dependency 33 of 255: dash:armel=0.5.11+git20210903+057cd650a4ed-8 Downloading dependency 34 of 255: libmagic1:armel=1:5.41-4 Downloading dependency 35 of 255: libbrotli1:armel=1.0.9-2+b4 Downloading dependency 36 of 255: libselinux1:armel=3.4-1+b1 Downloading dependency 37 of 255: libasan8:armel=12.2.0-1 Downloading dependency 38 of 255: samtools:armel=1.13-4 Downloading dependency 39 of 255: libpython3.10-minimal:armel=3.10.6-1 Downloading dependency 40 of 255: autoconf:armel=2.71-2 Downloading dependency 41 of 255: libcairo2:armel=1.16.0-6 Downloading dependency 42 of 255: libkmod2:armel=30+20220630-3 Downloading dependency 43 of 255: libsystemd0:armel=251.4-3 Downloading dependency 44 of 255: x11-common:armel=1:7.7+23 Downloading dependency 45 of 255: diffutils:armel=1:3.8-1 Downloading dependency 46 of 255: libbinutils:armel=2.38.90.20220713-2 Downloading dependency 47 of 255: python3-ruffus:armel=2.8.4-4 Downloading dependency 48 of 255: libfreetype6:armel=2.12.1+dfsg-3 Downloading dependency 49 of 255: libgcc-s1:armel=12.2.0-1 Downloading dependency 50 of 255: libctf-nobfd0:armel=2.38.90.20220713-2 Downloading dependency 51 of 255: libxaw7:armel=2:1.0.14-1 Downloading dependency 52 of 255: bsdutils:armel=1:2.38.1-1 Downloading dependency 53 of 255: libxmu6:armel=2:1.1.3-3 Downloading dependency 54 of 255: libmagic-mgc:armel=1:5.41-4 Downloading dependency 55 of 255: libblkid1:armel=2.38.1-1 Downloading dependency 56 of 255: libarchive-zip-perl:armel=1.68-1 Downloading dependency 57 of 255: libkrb5-3:armel=1.20-1 Downloading dependency 58 of 255: libk5crypto3:armel=1.20-1 Downloading dependency 59 of 255: libcurl3-gnutls:armel=7.85.0-1 Downloading dependency 60 of 255: libgcrypt20:armel=1.10.1-2 Downloading dependency 61 of 255: libpathplan4:armel=2.42.2-7 Downloading dependency 62 of 255: intltool-debian:armel=0.35.0+20060710.5 Downloading dependency 63 of 255: bash:armel=5.2~rc2-2 Downloading dependency 64 of 255: libhts3:armel=1.13+ds-2+b1 Downloading dependency 65 of 255: libcrypt-dev:armel=1:4.4.28-2 Downloading dependency 66 of 255: perl-modules-5.34:armel=5.34.0-5 Downloading dependency 67 of 255: libaudit1:armel=1:3.0.7-1+b1 Downloading dependency 68 of 255: libmd0:armel=1.0.4-2 Downloading dependency 69 of 255: libsqlite3-0:armel=3.39.2-1 Downloading dependency 70 of 255: libgmp10:armel=2:6.2.1+dfsg1-1 Downloading dependency 71 of 255: libelf1:armel=0.187-1 Downloading dependency 72 of 255: liblerc4:armel=4.0.0+ds-1 Downloading dependency 73 of 255: hostname:armel=3.23 Downloading dependency 74 of 255: mount:armel=2.38.1-1 Downloading dependency 75 of 255: file:armel=1:5.41-4 Downloading dependency 76 of 255: libudev1:armel=251.4-3 Downloading dependency 77 of 255: dpkg-dev:armel=1.21.9 Downloading dependency 78 of 255: fontconfig:armel=2.13.1-4.4 Downloading dependency 79 of 255: libpng16-16:armel=1.6.37-5 Downloading dependency 80 of 255: libx11-6:armel=2:1.8.1-2 Downloading dependency 81 of 255: sed:armel=4.8-1 Downloading dependency 82 of 255: libc-bin:armel=2.34-7 Downloading dependency 83 of 255: libdb5.3:armel=5.3.28+dfsg1-0.10 Downloading dependency 84 of 255: liblz4-1:armel=1.9.4-1 Downloading dependency 85 of 255: libmpdec3:armel=2.5.1-2 Downloading dependency 86 of 255: zlib1g:armel=1:1.2.11.dfsg-4.1 Downloading dependency 87 of 255: base-passwd:armel=3.6.0 Downloading dependency 88 of 255: grep:armel=3.7-1 Downloading dependency 89 of 255: libfribidi0:armel=1.0.8-2.1 Downloading dependency 90 of 255: libxpm4:armel=1:3.5.12-1 Downloading dependency 91 of 255: binutils-arm-linux-gnueabi:armel=2.38.90.20220713-2 Downloading dependency 92 of 255: libxcb1:armel=1.15-1 Downloading dependency 93 of 255: readline-common:armel=8.2~rc2-2 Downloading dependency 94 of 255: libsub-override-perl:armel=0.09-3 Downloading dependency 95 of 255: libmpc3:armel=1.2.1-2 Downloading dependency 96 of 255: libgraphite2-3:armel=1.3.14-1 Downloading dependency 97 of 255: libbsd0:armel=0.11.6-1 Downloading dependency 98 of 255: perl:armel=5.34.0-5 Downloading dependency 99 of 255: libcap2:armel=1:2.44-1 Downloading dependency 100 of 255: libapparmor1:armel=3.0.7-1 Downloading dependency 101 of 255: libuchardet0:armel=0.0.7-1 Downloading dependency 102 of 255: dh-autoreconf:armel=20 Downloading dependency 103 of 255: dwz:armel=0.14-1 Downloading dependency 104 of 255: libpython3.10-stdlib:armel=3.10.6-1 Downloading dependency 105 of 255: libgd3:armel=2.3.3-6 Downloading dependency 106 of 255: libisl23:armel=0.25-1 Downloading dependency 107 of 255: ucf:armel=3.0043 Downloading dependency 108 of 255: libgdbm6:armel=1.23-1+b1 Downloading dependency 109 of 255: liblocale-gettext-perl:armel=1.07-4+b2 Downloading dependency 110 of 255: linux-libc-dev:armel=5.18.16-1 Downloading dependency 111 of 255: findutils:armel=4.9.0-3 Downloading dependency 112 of 255: mawk:armel=1.3.4.20200120-3.1 Downloading dependency 113 of 255: autotools-dev:armel=20220109.1 Downloading dependency 114 of 255: gcc-12:armel=12.2.0-1 Downloading dependency 115 of 255: ncurses-base:armel=6.3+20220423-2 Downloading dependency 116 of 255: libthai0:armel=0.1.29-1 Downloading dependency 117 of 255: libmpfr6:armel=4.1.0-3 Downloading dependency 118 of 255: tar:armel=1.34+dfsg-1 Downloading dependency 119 of 255: libpsl5:armel=0.21.0-1.2 Downloading dependency 120 of 255: libc-dev-bin:armel=2.34-7 Downloading dependency 121 of 255: liblzma5:armel=5.2.5-2.1 Downloading dependency 122 of 255: make:armel=4.3-4.1 Downloading dependency 123 of 255: libxrender1:armel=1:0.9.10-1.1 Downloading dependency 124 of 255: libbamtools2.5.2:armel=2.5.2+dfsg-2 Downloading dependency 125 of 255: libmount1:armel=2.38.1-1 Downloading dependency 126 of 255: python3-distutils:armel=3.10.6-1 Downloading dependency 127 of 255: python3-lib2to3:armel=3.10.6-1 Downloading dependency 128 of 255: libsystemd-shared:armel=251.4-3 Downloading dependency 129 of 255: bsdextrautils:armel=2.38.1-1 Downloading dependency 130 of 255: libattr1:armel=1:2.5.1-1 Downloading dependency 131 of 255: libpango-1.0-0:armel=1.50.9+ds-1 Downloading dependency 132 of 255: fontconfig-config:armel=2.13.1-4.4 Downloading dependency 133 of 255: libxt6:armel=1:1.2.1-1 Downloading dependency 134 of 255: fonts-dejavu-core:armel=2.37-2Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel fonts-dejavu-core all 2.37-2 [1069 kB] Fetched 1069 kB in 0s (49.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpohiooeem/fonts-dejavu-core_2.37-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel binutils armel 2.38.90.20220713-2 [63.6 kB] Fetched 63.6 kB in 0s (5285 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbd60f5cy/binutils_2.38.90.20220713-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libicu71 armel 71.1-3 [8857 kB] Fetched 8857 kB in 0s (99.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpovwte0md/libicu71_71.1-3_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libubsan1 armel 12.2.0-1 [863 kB] Fetched 863 kB in 0s (32.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw_5x3tbo/libubsan1_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpcre3 armel 2:8.39-14 [318 kB] Fetched 318 kB in 0s (27.1 MB/s) dpkg-name: info: moved 'libpcre3_2%3a8.39-14_armel.deb' to '/srv/rebuilderd/tmp/tmpym2w9xvp/libpcre3_8.39-14_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libsm6 armel 2:1.2.3-1 [33.1 kB] Fetched 33.1 kB in 0s (3025 kB/s) dpkg-name: info: moved 'libsm6_2%3a1.2.3-1_armel.deb' to '/srv/rebuilderd/tmp/tmp0yf5ue3p/libsm6_1.2.3-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel lsb-base all 11.2 [29.1 kB] Fetched 29.1 kB in 0s (2202 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplnk2e2h5/lsb-base_11.2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libreadline8 armel 8.2~rc2-2 [148 kB] Fetched 148 kB in 0s (7816 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplqkz7869/libreadline8_8.2~rc2-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel debianutils armel 5.7-0.3 [101 kB] Fetched 101 kB in 0s (7285 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzo54y_dw/debianutils_5.7-0.3_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libatomic1 armel 12.2.0-1 [9144 B] Fetched 9144 B in 0s (450 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi7g7lk34/libatomic1_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libip4tc2 armel 1.8.8-1 [32.8 kB] Fetched 32.8 kB in 0s (2498 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt_ex8tjf/libip4tc2_1.8.8-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libctf0 armel 2.38.90.20220713-2 [79.7 kB] Fetched 79.7 kB in 0s (2908 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi98ym919/libctf0_2.38.90.20220713-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libexpat1 armel 2.4.8-1 [84.8 kB] Fetched 84.8 kB in 0s (7314 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1rz4nbmr/libexpat1_2.4.8-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel base-files armel 12.2 [70.1 kB] Fetched 70.1 kB in 0s (3763 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpduxs_sen/base-files_12.2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libgdbm-compat4 armel 1.23-1+b1 [58.5 kB] Fetched 58.5 kB in 0s (3253 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpavkdm4wo/libgdbm-compat4_1.23-1+b1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libx11-data all 2:1.8.1-2 [308 kB] Fetched 308 kB in 0s (26.5 MB/s) dpkg-name: info: moved 'libx11-data_2%3a1.8.1-2_all.deb' to '/srv/rebuilderd/tmp/tmp1qsg8h9y/libx11-data_1.8.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libncurses6 armel 6.3+20220423-2 [81.2 kB] Fetched 81.2 kB in 0s (4988 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmon4wb_s/libncurses6_6.3+20220423-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libice6 armel 2:1.0.10-1 [51.6 kB] Fetched 51.6 kB in 0s (5003 kB/s) dpkg-name: info: moved 'libice6_2%3a1.0.10-1_armel.deb' to '/srv/rebuilderd/tmp/tmp0xkdrmd_/libice6_1.0.10-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libfontconfig1 armel 2.13.1-4.4 [333 kB] Fetched 333 kB in 0s (19.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8m78lkvn/libfontconfig1_2.13.1-4.4_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpipeline1 armel 1.5.6-2 [34.1 kB] Fetched 34.1 kB in 0s (1981 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6h2jf14t/libpipeline1_1.5.6-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220921T235202Z bookworm/main armel gettext armel 0.21-9 [1236 kB] Fetched 1236 kB in 0s (86.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0wkhmsmu/gettext_0.21-9_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libc6 armel 2.34-7 [2384 kB] Fetched 2384 kB in 0s (102 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8l7hoc4c/libc6_2.34-7_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel patch armel 2.7.6-7 [125 kB] Fetched 125 kB in 0s (6669 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6jbkberj/patch_2.7.6-7_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel po-debconf all 1.0.21+nmu1 [248 kB] Fetched 248 kB in 0s (16.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpofodaq6r/po-debconf_1.0.21+nmu1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel sensible-utils all 0.0.17 [21.5 kB] Fetched 21.5 kB in 0s (1719 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsebpxfwk/sensible-utils_0.0.17_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel python3-pysam armel 0.17.0+ds-2+b2 [1418 kB] Fetched 1418 kB in 0s (43.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy1o7w337/python3-pysam_0.17.0+ds-2+b2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libtirpc3 armel 1.3.3+ds-1 [72.0 kB] Fetched 72.0 kB in 0s (2413 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcv0eg8eg/libtirpc3_1.3.3+ds-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libzstd1 armel 1.5.2+dfsg-1 [237 kB] Fetched 237 kB in 0s (11.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfke9y_dy/libzstd1_1.5.2+dfsg-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel python3-minimal armel 3.10.6-1 [38.7 kB] Fetched 38.7 kB in 0s (2073 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuzstjws1/python3-minimal_3.10.6-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220921T235202Z bookworm/main armel gettext-base armel 0.21-9 [172 kB] Fetched 172 kB in 0s (11.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4ka572k_/gettext-base_0.21-9_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libgts-0.7-5 armel 0.7.6+darcs121130-5 [152 kB] Fetched 152 kB in 0s (8320 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt1ml4orv/libgts-0.7-5_0.7.6+darcs121130-5_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libxcb-render0 armel 1.15-1 [114 kB] Fetched 114 kB in 0s (6069 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp776592m4/libxcb-render0_1.15-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel help2man armel 1.49.2 [202 kB] Fetched 202 kB in 0s (5265 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgswplr4v/help2man_1.49.2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpython3-stdlib armel 3.10.6-1 [21.7 kB] Fetched 21.7 kB in 0s (750 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7tvq86qu/libpython3-stdlib_3.10.6-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libxext6 armel 2:1.3.4-1 [47.9 kB] Fetched 47.9 kB in 0s (2056 kB/s) dpkg-name: info: moved 'libxext6_2%3a1.3.4-1_armel.deb' to '/srv/rebuilderd/tmp/tmpjjzgum2n/libxext6_1.3.4-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel coreutils armel 8.32-4.1 [2702 kB] Fetched 2702 kB in 0s (113 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpax2a8czv/coreutils_8.32-4.1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libdpkg-perl all 1.21.9 [1621 kB] Fetched 1621 kB in 0s (53.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdcekxiw6/libdpkg-perl_1.21.9_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libgomp1 armel 12.2.0-1 [99.1 kB] Fetched 99.1 kB in 0s (5104 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdoqekozh/libgomp1_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libldap-2.5-0 armel 2.5.12+dfsg-2+b1 [199 kB] Fetched 199 kB in 0s (12.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzttxexbs/libldap-2.5-0_2.5.12+dfsg-2+b1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpam-modules armel 1.5.2-2 [314 kB] Fetched 314 kB in 0s (17.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxqgxh9yj/libpam-modules_1.5.2-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libsasl2-2 armel 2.1.28+dfsg-7 [70.1 kB] Fetched 70.1 kB in 0s (4254 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa1aq0fwt/libsasl2-2_2.1.28+dfsg-7_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libgvpr2 armel 2.42.2-7 [185 kB] Fetched 185 kB in 0s (13.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnie_eb8u/libgvpr2_2.42.2-7_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libhogweed6 armel 3.8.1-2 [315 kB] Fetched 315 kB in 0s (14.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpebmsgpwz/libhogweed6_3.8.1-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpam-modules-bin armel 1.5.2-2 [110 kB] Fetched 110 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnbli_2_m/libpam-modules-bin_1.5.2-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel dpkg armel 1.21.9 [2505 kB] Fetched 2505 kB in 0s (129 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkhudxnqr/dpkg_1.21.9_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel build-essential armel 12.9 [7708 B] Fetched 7708 B in 0s (392 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8yy9fef7/build-essential_12.9_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel ncurses-bin armel 6.3+20220423-2 [433 kB] Fetched 433 kB in 0s (24.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl4lbru1o/ncurses-bin_6.3+20220423-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libc6-dev armel 2.34-7 [1465 kB] Fetched 1465 kB in 0s (60.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptkuh77xa/libc6-dev_2.34-7_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libssl3 armel 3.0.5-2 [1643 kB] Fetched 1643 kB in 0s (44.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4l_bhlmg/libssl3_3.0.5-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libjpeg62-turbo armel 1:2.1.2-1 [146 kB] Fetched 146 kB in 0s (6975 kB/s) dpkg-name: info: moved 'libjpeg62-turbo_1%3a2.1.2-1_armel.deb' to '/srv/rebuilderd/tmp/tmpw7s8yez_/libjpeg62-turbo_2.1.2-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel init-system-helpers all 1.64 [49.2 kB] Fetched 49.2 kB in 0s (3127 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwslim38g/init-system-helpers_1.64_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220921T235202Z bookworm/main armel gcc armel 4:12.2.0-1 [5204 B] Fetched 5204 B in 0s (281 kB/s) dpkg-name: info: moved 'gcc_4%3a12.2.0-1_armel.deb' to '/srv/rebuilderd/tmp/tmpcwpxgj46/gcc_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel sysvinit-utils armel 3.04-1 [25.7 kB] Fetched 25.7 kB in 0s (1257 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp86mxvgb_/sysvinit-utils_3.04-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libtool all 2.4.7-4 [526 kB] Fetched 526 kB in 0s (38.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw6nlusku/libtool_2.4.7-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libwebp7 armel 1.2.2-2+b1 [223 kB] Fetched 223 kB in 0s (15.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2_q_i9c9/libwebp7_1.2.2-2+b1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel m4 armel 1.4.19-1 [269 kB] Fetched 269 kB in 0s (14.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppdjiwwe1/m4_1.4.19-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libgvc6 armel 2.42.2-7 [633 kB] Fetched 633 kB in 0s (32.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpua4tddok/libgvc6_2.42.2-7_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libjbig0 armel 2.1-3.1+b2 [27.8 kB] Fetched 27.8 kB in 0s (903 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyusz13wa/libjbig0_2.1-3.1+b2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libtirpc-dev armel 1.3.3+ds-1 [182 kB] Fetched 182 kB in 0s (14.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo70yxx2b/libtirpc-dev_1.3.3+ds-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libsparsehash-dev all 2.0.3-2 [76.8 kB] Fetched 76.8 kB in 0s (5138 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd04fk3fq/libsparsehash-dev_2.0.3-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel python3 armel 3.10.6-1 [38.2 kB] Fetched 38.2 kB in 0s (3390 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnz30b6dc/python3_3.10.6-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpam-runtime all 1.5.2-2 [200 kB] Fetched 200 kB in 0s (14.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr81bkc5z/libpam-runtime_1.5.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libjson-c5 armel 0.16-1 [40.4 kB] Fetched 40.4 kB in 0s (3227 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpftyozozv/libjson-c5_0.16-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel dh-python all 5.20220819 [114 kB] Fetched 114 kB in 0s (6954 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_i4t6hxn/dh-python_5.20220819_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libxml2 armel 2.9.14+dfsg-1+b1 [593 kB] Fetched 593 kB in 0s (51.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf82vgen_/libxml2_2.9.14+dfsg-1+b1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libunistring2 armel 1.0-1 [403 kB] Fetched 403 kB in 0s (15.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz_78tldn/libunistring2_1.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel librtmp1 armel 2.4+20151223.gitfa8646d.1-2+b2 [55.1 kB] Fetched 55.1 kB in 0s (3406 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2ykwvb_x/librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel zlib1g-dev armel 1:1.2.11.dfsg-4.1 [184 kB] Fetched 184 kB in 0s (11.5 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.2.11.dfsg-4.1_armel.deb' to '/srv/rebuilderd/tmp/tmpzh4mktyx/zlib1g-dev_1.2.11.dfsg-4.1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libgcc-12-dev armel 12.2.0-1 [735 kB] Fetched 735 kB in 0s (30.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplhwqcxds/libgcc-12-dev_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libdevmapper1.02.1 armel 2:1.02.185-1 [136 kB] Fetched 136 kB in 0s (9212 kB/s) dpkg-name: info: moved 'libdevmapper1.02.1_2%3a1.02.185-1_armel.deb' to '/srv/rebuilderd/tmp/tmpwwa2nz6n/libdevmapper1.02.1_1.02.185-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libcgraph6 armel 2.42.2-7 [78.6 kB] Fetched 78.6 kB in 0s (5510 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphi8q818q/libcgraph6_2.42.2-7_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpixman-1-0 armel 0.40.0-1 [483 kB] Fetched 483 kB in 0s (22.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp30vdhnc1/libpixman-1-0_0.40.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libgpg-error0 armel 1.45-2 [72.1 kB] Fetched 72.1 kB in 0s (5791 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7q1n2t_n/libgpg-error0_1.45-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libdebconfclient0 armel 0.264 [50.7 kB] Fetched 50.7 kB in 0s (2796 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdpgbeu0f/libdebconfclient0_0.264_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libcap-ng0 armel 0.8.3-1+b1 [17.7 kB] Fetched 17.7 kB in 0s (1526 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4ssq4far/libcap-ng0_0.8.3-1+b1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel automake all 1:1.16.5-1.3 [823 kB] Fetched 823 kB in 0s (58.9 MB/s) dpkg-name: info: moved 'automake_1%3a1.16.5-1.3_all.deb' to '/srv/rebuilderd/tmp/tmps1h5a678/automake_1.16.5-1.3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libdatrie1 armel 0.2.13-2 [39.6 kB] Fetched 39.6 kB in 0s (3787 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp060gwy4i/libdatrie1_0.2.13-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB] Fetched 26.6 kB in 0s (1809 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2qesezam/libfile-stripnondeterminism-perl_1.13.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libsasl2-modules-db armel 2.1.28+dfsg-7 [37.3 kB] Fetched 37.3 kB in 0s (2535 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3mepixxr/libsasl2-modules-db_2.1.28+dfsg-7_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel python3.10 armel 3.10.6-1 [545 kB] Fetched 545 kB in 0s (34.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_5k6ti70/python3.10_3.10.6-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel media-types all 8.0.0 [33.4 kB] Fetched 33.4 kB in 0s (2150 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk0vdihrh/media-types_8.0.0_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpangocairo-1.0-0 armel 1.50.9+ds-1 [60.4 kB] Fetched 60.4 kB in 0s (3721 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps2x59jq6/libpangocairo-1.0-0_1.50.9+ds-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libtiff5 armel 4.4.0-4 [293 kB] Fetched 293 kB in 0s (23.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmv05qh5k/libtiff5_4.4.0-4_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libtinfo6 armel 6.3+20220423-2 [337 kB] Fetched 337 kB in 0s (25.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpydlqw3zu/libtinfo6_6.3+20220423-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libxau6 armel 1:1.0.9-1 [19.0 kB] Fetched 19.0 kB in 0s (1756 kB/s) dpkg-name: info: moved 'libxau6_1%3a1.0.9-1_armel.deb' to '/srv/rebuilderd/tmp/tmpp07b5sk0/libxau6_1.0.9-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libacl1 armel 2.3.1-1 [28.4 kB] Fetched 28.4 kB in 0s (2572 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpodeg5jxp/libacl1_2.3.1-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libseccomp2 armel 2.5.4-1+b1 [47.5 kB] Fetched 47.5 kB in 0s (3348 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyg4c9cv7/libseccomp2_2.5.4-1+b1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libgnutls30 armel 3.7.7-2 [1324 kB] Fetched 1324 kB in 0s (60.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1psa9bev/libgnutls30_3.7.7-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel liblab-gamut1 armel 2.42.2-7 [221 kB] Fetched 221 kB in 0s (18.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpygrjuzaa/liblab-gamut1_2.42.2-7_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel dmsetup armel 2:1.02.185-1 [92.5 kB] Fetched 92.5 kB in 0s (8084 kB/s) dpkg-name: info: moved 'dmsetup_2%3a1.02.185-1_armel.deb' to '/srv/rebuilderd/tmp/tmp5fxgxbsp/dmsetup_1.02.185-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libncursesw6 armel 6.3+20220423-2 [106 kB] Fetched 106 kB in 0s (6179 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0w0ozi84/libncursesw6_6.3+20220423-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libstdc++-12-dev armel 12.2.0-1 [2081 kB] Fetched 2081 kB in 0s (85.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbq32qak2/libstdc++-12-dev_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libtasn1-6 armel 4.18.0-4 [50.6 kB] Fetched 50.6 kB in 0s (3167 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplc2qbly3/libtasn1-6_4.18.0-4_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libnghttp2-14 armel 1.49.0-1 [70.5 kB] Fetched 70.5 kB in 0s (4019 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5rk121m9/libnghttp2-14_1.49.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libnsl-dev armel 1.3.0-2 [61.7 kB] Fetched 61.7 kB in 0s (4884 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzq63_46z/libnsl-dev_1.3.0-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel systemd armel 251.4-3 [2762 kB] Fetched 2762 kB in 0s (30.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpak02omnf/systemd_251.4-3_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libuuid1 armel 2.38.1-1 [84.8 kB] Fetched 84.8 kB in 0s (1992 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb7_fp9qg/libuuid1_2.38.1-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220921T235202Z bookworm/main armel libbamtools-dev armel 2.5.2+dfsg-2 [195 kB] Fetched 195 kB in 0s (3662 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpteiqoxif/libbamtools-dev_2.5.2+dfsg-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libthai-data all 0.1.29-1 [176 kB] Fetched 176 kB in 0s (7367 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplu_zae23/libthai-data_0.1.29-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel debconf all 1.5.79 [143 kB] Fetched 143 kB in 0s (8711 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnrj1c2w6/debconf_1.5.79_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libcdt5 armel 2.42.2-7 [59.6 kB] Fetched 59.6 kB in 0s (4372 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbzy43tao/libcdt5_2.42.2-7_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libnettle8 armel 3.8.1-2 [294 kB] Fetched 294 kB in 0s (14.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmft9artm/libnettle8_3.8.1-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libperl5.34 armel 5.34.0-5 [3455 kB] Fetched 3455 kB in 0s (117 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxovophl4/libperl5.34_5.34.0-5_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220921T235202Z bookworm/main armel cpp armel 4:12.2.0-1 [20.0 kB] Fetched 20.0 kB in 0s (1566 kB/s) dpkg-name: info: moved 'cpp_4%3a12.2.0-1_armel.deb' to '/srv/rebuilderd/tmp/tmp_m58rii9/cpp_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libhtscodecs2 armel 1.2.2-1 [54.0 kB] Fetched 54.0 kB in 0s (3805 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpog0e_cm2/libhtscodecs2_1.2.2-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel graphviz armel 2.42.2-7 [528 kB] Fetched 528 kB in 0s (34.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8d6wjgtn/graphviz_2.42.2-7_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libbz2-1.0 armel 1.0.8-5 [44.8 kB] Fetched 44.8 kB in 0s (3544 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3wr5jjdp/libbz2-1.0_1.0.8-5_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libidn2-0 armel 2.3.3-1+b1 [120 kB] Fetched 120 kB in 0s (9735 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdm459emz/libidn2-0_2.3.3-1+b1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libcrypt1 armel 1:4.4.28-2 [97.6 kB] Fetched 97.6 kB in 0s (6727 kB/s) dpkg-name: info: moved 'libcrypt1_1%3a4.4.28-2_armel.deb' to '/srv/rebuilderd/tmp/tmp13e3onp7/libcrypt1_4.4.28-2_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libsmartcols1 armel 2.38.1-1 [150 kB] Fetched 150 kB in 0s (10.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1adc5v05/libsmartcols1_2.38.1-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libgssapi-krb5-2 armel 1.20-1 [143 kB] Fetched 143 kB in 0s (10.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxk2bpjzc/libgssapi-krb5-2_1.20-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220921T235202Z bookworm/main armel g++ armel 4:12.2.0-1 [1620 B] Fetched 1620 B in 0s (89.7 kB/s) dpkg-name: info: moved 'g++_4%3a12.2.0-1_armel.deb' to '/srv/rebuilderd/tmp/tmp23z1ixde/g++_12.2.0-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libargon2-1 armel 0~20171227-0.3 [19.5 kB] Fetched 19.5 kB in 0s (1335 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplmg4s1da/libargon2-1_0~20171227-0.3_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libfdisk1 armel 2.38.1-1 [238 kB] Fetched 238 kB in 0s (13.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptvc3rlyg/libfdisk1_2.38.1-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel debhelper all 13.9.1 [1071 kB] Fetched 1071 kB in 0s (59.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8bznfn6w/debhelper_13.9.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libltdl7 armel 2.4.7-4 [399 kB] Fetched 399 kB in 0s (14.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpogguc9vy/libltdl7_2.4.7-4_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libtirpc-common all 1.3.3+ds-1 [14.0 kB] Fetched 14.0 kB in 0s (958 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr59rf8vb/libtirpc-common_1.3.3+ds-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel libpcre2-8-0 armel 10.40-1 [222 kB] Fetched 222 kB in 0s (15.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz5q52f8a/libpcre2-8-0_10.40-1_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel dh-strip-nondeterminism all 1.13.0-1 [15.8 kB] Fetched 15.8 kB in 0s (1457 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuc5rxp6z/dh-strip-nondeterminism_1.13.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel perl-base armel 5.34.0-5 [1474 kB] Fetched 1474 kB in 0s (61.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppm_2i077/perl-base_5.34.0-5_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel groff-base armel 1.22.4-8 [840 kB] Fetched 840 kB in 0s (64.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptii3sgml/groff-base_1.22.4-8_armel.deb' Get:1 http://snapshot.debian.org/archive/debian/20220903T155935Z bookworm/main armel gzip armel 1.12-1 [137 kB] Fetched 137 kB in 0s (7948 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7xyt_jog/gzip_1.12-1_armel.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/tmpjw3vja3q/cache directory, not in ".." as indicated by the message above! I: automatically chosen mode: unshare I: armel is different from arm64 but can be executed natively I: using /srv/rebuilderd/tmp/mmdebstrap.tII8zHIu_F as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.tII8zHIu_F 127.0.0.1 - - [28/Jul/2025 23:57:46] code 404, message File not found 127.0.0.1 - - [28/Jul/2025 23:57:46] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:45629 ./ InRelease 127.0.0.1 - - [28/Jul/2025 23:57:46] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:45629 ./ Release [462 B] 127.0.0.1 - - [28/Jul/2025 23:57:46] code 404, message File not found 127.0.0.1 - - [28/Jul/2025 23:57:46] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:45629 ./ Release.gpg 127.0.0.1 - - [28/Jul/2025 23:57:46] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:45629 ./ Packages [309 kB] Fetched 310 kB in 0s (10.1 MB/s) Reading package lists... no package providing usr-is-merged found -- not running merged-usr setup hook I: skipping apt-get update because it was already run I: downloading packages with apt... 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./gcc-12-base_12.2.0-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libc6_2.34-7_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libgcc-s1_12.2.0-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./mawk_1.3.4.20200120-3.1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./base-files_12.2_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libtinfo6_6.3%2b20220423-2_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./debianutils_5.7-0.3_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./bash_5.2%7erc2-2_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libcap2_2.44-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libgpg-error0_1.45-2_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libgcrypt20_1.10.1-2_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./liblz4-1_1.9.4-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./liblzma5_5.2.5-2.1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libzstd1_1.5.2%2bdfsg-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libsystemd0_251.4-3_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./bsdutils_2.38.1-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libacl1_2.3.1-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libattr1_2.5.1-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libgmp10_6.2.1%2bdfsg1-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libpcre2-8-0_10.40-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libselinux1_3.4-1%2bb1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./coreutils_8.32-4.1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libbz2-1.0_1.0.8-5_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./zlib1g_1.2.11.dfsg-4.1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./tar_1.34%2bdfsg-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./dpkg_1.21.9_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./dash_0.5.11%2bgit20210903%2b057cd650a4ed-8_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./diffutils_3.8-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./findutils_4.9.0-3_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libpcre3_8.39-14_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./grep_3.7-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./gzip_1.12-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./hostname_3.23_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libaudit-common_3.0.7-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libcap-ng0_0.8.3-1%2bb1_armel.deb HTTP/1.1" 200 - 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127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./sed_4.8-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libblkid1_2.38.1-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libmount1_2.38.1-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libsmartcols1_2.38.1-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libudev1_251.4-3_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libuuid1_2.38.1-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./util-linux-extra_2.38.1-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./util-linux_2.38.1-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libdebconfclient0_0.264_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./base-passwd_3.6.0_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./init-system-helpers_1.64_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./libc-bin_2.34-7_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./ncurses-base_6.3%2b20220423-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./lsb-base_11.2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:57:47] "GET /./sysvinit-utils_3.04-1_armel.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.tII8zHIu_F 127.0.0.1 - - [28/Jul/2025 23:57:49] code 404, message File not found 127.0.0.1 - - [28/Jul/2025 23:57:49] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:45629 ./ InRelease 127.0.0.1 - - [28/Jul/2025 23:57:49] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:45629 ./ Release 127.0.0.1 - - [28/Jul/2025 23:57:49] code 404, message File not found 127.0.0.1 - - [28/Jul/2025 23:57:49] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:45629 ./ Release.gpg Reading package lists... no package providing usr-is-merged found -- not running merged-usr extract hook I: installing essential packages... I: running --essential-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/essential00.sh /srv/rebuilderd/tmp/mmdebstrap.tII8zHIu_F no package called usr-is-merged is installed -- not running merged-usr essential hook I: installing remaining packages inside the chroot... 127.0.0.1 - - [28/Jul/2025 23:58:02] "GET /./liblocale-gettext-perl_1.07-4%2bb2_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:58:02] "GET /./mount_2.38.1-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:58:02] "GET /./libargon2-1_0%7e20171227-0.3_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:58:02] "GET /./dmsetup_1.02.185-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:58:02] "GET /./libdevmapper1.02.1_1.02.185-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:58:02] "GET /./libjson-c5_0.16-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:58:02] "GET /./libatomic1_12.2.0-1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:58:02] "GET /./libssl3_3.0.5-2_armel.deb HTTP/1.1" 200 - 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- [28/Jul/2025 23:58:03] "GET /./python3-lib2to3_3.10.6-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:58:03] "GET /./python3-distutils_3.10.6-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:58:03] "GET /./python3-pysam_0.17.0%2bds-2%2bb2_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:58:03] "GET /./help2man_1.49.2_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:58:03] "GET /./libsparsehash-dev_2.0.3-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:58:03] "GET /./dh-python_5.20220819_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:58:03] "GET /./zlib1g-dev_1.2.11.dfsg-4.1_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:58:03] "GET /./libbamtools-dev_2.5.2%2bdfsg-2_armel.deb HTTP/1.1" 200 - 127.0.0.1 - - [28/Jul/2025 23:58:03] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmpjw3vja3q/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.tII8zHIu_F Reading package lists... Building dependency tree... Reading state information... bzip2 is already the newest version (1.0.8-5). bzip2 set to manually installed. libkeyutils1 is already the newest version (1.6.3-1). libkeyutils1 set to manually installed. gcc-12-base is already the newest version (12.2.0-1). util-linux-extra is already the newest version (2.38.1-1). libkrb5support0 is already the newest version (1.20-1). libkrb5support0 set to manually installed. libp11-kit0 is already the newest version (0.24.1-1). libp11-kit0 set to manually installed. g++-12 is already the newest version (12.2.0-1). g++-12 set to manually installed. libdebhelper-perl is already the newest version (13.9.1). libdebhelper-perl set to manually installed. cpp-12 is already the newest version (12.2.0-1). cpp-12 set to manually installed. libdeflate0 is already the newest version (1.12-1). libdeflate0 set to manually installed. login is already the newest version (1:4.11.1+dfsg1-2). rpcsvc-proto is already the newest version (1.4.2-4). rpcsvc-proto set to manually installed. libpam0g is already the newest version (1.5.2-2). python3.10-minimal is already the newest version (3.10.6-1). python3.10-minimal set to manually installed. libglib2.0-0 is already the newest version (2.73.3-3). libglib2.0-0 set to manually installed. libstdc++6 is already the newest version (12.2.0-1). libstdc++6 set to manually installed. man-db is already the newest version (2.10.2-2). man-db set to manually installed. libnsl2 is already the newest version (1.3.0-2). libnsl2 set to manually installed. libxcb-shm0 is already the newest version (1.15-1). libxcb-shm0 set to manually installed. libxdmcp6 is already the newest version (1:1.1.2-3). libxdmcp6 set to manually installed. binutils-common is already the newest version (2.38.90.20220713-2). binutils-common set to manually installed. util-linux is already the newest version (2.38.1-1). libcc1-0 is already the newest version (12.2.0-1). libcc1-0 set to manually installed. libssh2-1 is already the newest version (1.10.0-3+b1). libssh2-1 set to manually installed. autopoint is already the newest version (0.21-9). autopoint set to manually installed. libffi8 is already the newest version (3.4.2-4). libffi8 set to manually installed. libaudit-common is already the newest version (1:3.0.7-1). libcryptsetup12 is already the newest version (2:2.5.0-2). libcryptsetup12 set to manually installed. libpangoft2-1.0-0 is already the newest version (1.50.9+ds-1). libpangoft2-1.0-0 set to manually installed. xz-utils is already the newest version (5.2.5-2.1). xz-utils set to manually installed. libharfbuzz0b is already the newest version (2.7.4-1+b1). libharfbuzz0b set to manually installed. libcom-err2 is already the newest version (1.46.5-2). libcom-err2 set to manually installed. dash is already the newest version (0.5.11+git20210903+057cd650a4ed-8). libmagic1 is already the newest version (1:5.41-4). libmagic1 set to manually installed. libbrotli1 is already the newest version (1.0.9-2+b4). libbrotli1 set to manually installed. libselinux1 is already the newest version (3.4-1+b1). libasan8 is already the newest version (12.2.0-1). libasan8 set to manually installed. samtools is already the newest version (1.13-4). samtools set to manually installed. libpython3.10-minimal is already the newest version (3.10.6-1). libpython3.10-minimal set to manually installed. autoconf is already the newest version (2.71-2). autoconf set to manually installed. libcairo2 is already the newest version (1.16.0-6). libcairo2 set to manually installed. libkmod2 is already the newest version (30+20220630-3). libkmod2 set to manually installed. libsystemd0 is already the newest version (251.4-3). x11-common is already the newest version (1:7.7+23). x11-common set to manually installed. diffutils is already the newest version (1:3.8-1). libbinutils is already the newest version (2.38.90.20220713-2). libbinutils set to manually installed. python3-ruffus is already the newest version (2.8.4-4). python3-ruffus set to manually installed. libfreetype6 is already the newest version (2.12.1+dfsg-3). libfreetype6 set to manually installed. libgcc-s1 is already the newest version (12.2.0-1). libctf-nobfd0 is already the newest version (2.38.90.20220713-2). libctf-nobfd0 set to manually installed. libxaw7 is already the newest version (2:1.0.14-1). libxaw7 set to manually installed. bsdutils is already the newest version (1:2.38.1-1). libxmu6 is already the newest version (2:1.1.3-3). libxmu6 set to manually installed. libmagic-mgc is already the newest version (1:5.41-4). libmagic-mgc set to manually installed. libblkid1 is already the newest version (2.38.1-1). libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libkrb5-3 is already the newest version (1.20-1). libkrb5-3 set to manually installed. libk5crypto3 is already the newest version (1.20-1). libk5crypto3 set to manually installed. libcurl3-gnutls is already the newest version (7.85.0-1). libcurl3-gnutls set to manually installed. libgcrypt20 is already the newest version (1.10.1-2). libpathplan4 is already the newest version (2.42.2-7). libpathplan4 set to manually installed. intltool-debian is already the newest version (0.35.0+20060710.5). intltool-debian set to manually installed. bash is already the newest version (5.2~rc2-2). libhts3 is already the newest version (1.13+ds-2+b1). libhts3 set to manually installed. libcrypt-dev is already the newest version (1:4.4.28-2). libcrypt-dev set to manually installed. perl-modules-5.34 is already the newest version (5.34.0-5). perl-modules-5.34 set to manually installed. libaudit1 is already the newest version (1:3.0.7-1+b1). libmd0 is already the newest version (1.0.4-2). libmd0 set to manually installed. libsqlite3-0 is already the newest version (3.39.2-1). libsqlite3-0 set to manually installed. libgmp10 is already the newest version (2:6.2.1+dfsg1-1). libelf1 is already the newest version (0.187-1). libelf1 set to manually installed. liblerc4 is already the newest version (4.0.0+ds-1). liblerc4 set to manually installed. hostname is already the newest version (3.23). mount is already the newest version (2.38.1-1). mount set to manually installed. file is already the newest version (1:5.41-4). file set to manually installed. libudev1 is already the newest version (251.4-3). dpkg-dev is already the newest version (1.21.9). dpkg-dev set to manually installed. fontconfig is already the newest version (2.13.1-4.4). fontconfig set to manually installed. libpng16-16 is already the newest version (1.6.37-5). libpng16-16 set to manually installed. libx11-6 is already the newest version (2:1.8.1-2). libx11-6 set to manually installed. sed is already the newest version (4.8-1). libc-bin is already the newest version (2.34-7). libdb5.3 is already the newest version (5.3.28+dfsg1-0.10). liblz4-1 is already the newest version (1.9.4-1). libmpdec3 is already the newest version (2.5.1-2). libmpdec3 set to manually installed. zlib1g is already the newest version (1:1.2.11.dfsg-4.1). base-passwd is already the newest version (3.6.0). grep is already the newest version (3.7-1). libfribidi0 is already the newest version (1.0.8-2.1). libfribidi0 set to manually installed. libxpm4 is already the newest version (1:3.5.12-1). libxpm4 set to manually installed. binutils-arm-linux-gnueabi is already the newest version (2.38.90.20220713-2). binutils-arm-linux-gnueabi set to manually installed. libxcb1 is already the newest version (1.15-1). libxcb1 set to manually installed. readline-common is already the newest version (8.2~rc2-2). readline-common set to manually installed. libsub-override-perl is already the newest version (0.09-3). libsub-override-perl set to manually installed. libmpc3 is already the newest version (1.2.1-2). libmpc3 set to manually installed. libgraphite2-3 is already the newest version (1.3.14-1). libgraphite2-3 set to manually installed. libbsd0 is already the newest version (0.11.6-1). libbsd0 set to manually installed. perl is already the newest version (5.34.0-5). perl set to manually installed. libcap2 is already the newest version (1:2.44-1). libapparmor1 is already the newest version (3.0.7-1). libapparmor1 set to manually installed. libuchardet0 is already the newest version (0.0.7-1). libuchardet0 set to manually installed. dh-autoreconf is already the newest version (20). dh-autoreconf set to manually installed. dwz is already the newest version (0.14-1). dwz set to manually installed. libpython3.10-stdlib is already the newest version (3.10.6-1). libpython3.10-stdlib set to manually installed. libgd3 is already the newest version (2.3.3-6). libgd3 set to manually installed. libisl23 is already the newest version (0.25-1). libisl23 set to manually installed. ucf is already the newest version (3.0043). ucf set to manually installed. libgdbm6 is already the newest version (1.23-1+b1). libgdbm6 set to manually installed. liblocale-gettext-perl is already the newest version (1.07-4+b2). liblocale-gettext-perl set to manually installed. linux-libc-dev is already the newest version (5.18.16-1). linux-libc-dev set to manually installed. findutils is already the newest version (4.9.0-3). mawk is already the newest version (1.3.4.20200120-3.1). autotools-dev is already the newest version (20220109.1). autotools-dev set to manually installed. gcc-12 is already the newest version (12.2.0-1). gcc-12 set to manually installed. ncurses-base is already the newest version (6.3+20220423-2). libthai0 is already the newest version (0.1.29-1). libthai0 set to manually installed. libmpfr6 is already the newest version (4.1.0-3). libmpfr6 set to manually installed. tar is already the newest version (1.34+dfsg-1). libpsl5 is already the newest version (0.21.0-1.2). libpsl5 set to manually installed. libc-dev-bin is already the newest version (2.34-7). libc-dev-bin set to manually installed. liblzma5 is already the newest version (5.2.5-2.1). make is already the newest version (4.3-4.1). make set to manually installed. libxrender1 is already the newest version (1:0.9.10-1.1). libxrender1 set to manually installed. libbamtools2.5.2 is already the newest version (2.5.2+dfsg-2). libbamtools2.5.2 set to manually installed. libmount1 is already the newest version (2.38.1-1). python3-distutils is already the newest version (3.10.6-1). python3-distutils set to manually installed. python3-lib2to3 is already the newest version (3.10.6-1). python3-lib2to3 set to manually installed. libsystemd-shared is already the newest version (251.4-3). libsystemd-shared set to manually installed. bsdextrautils is already the newest version (2.38.1-1). bsdextrautils set to manually installed. libattr1 is already the newest version (1:2.5.1-1). libpango-1.0-0 is already the newest version (1.50.9+ds-1). libpango-1.0-0 set to manually installed. fontconfig-config is already the newest version (2.13.1-4.4). fontconfig-config set to manually installed. libxt6 is already the newest version (1:1.2.1-1). libxt6 set to manually installed. fonts-dejavu-core is already the newest version (2.37-2). fonts-dejavu-core set to manually installed. binutils is already the newest version (2.38.90.20220713-2). binutils set to manually installed. libicu71 is already the newest version (71.1-3). libicu71 set to manually installed. libubsan1 is already the newest version (12.2.0-1). libubsan1 set to manually installed. libpcre3 is already the newest version (2:8.39-14). libsm6 is already the newest version (2:1.2.3-1). libsm6 set to manually installed. lsb-base is already the newest version (11.2). libreadline8 is already the newest version (8.2~rc2-2). libreadline8 set to manually installed. debianutils is already the newest version (5.7-0.3). libatomic1 is already the newest version (12.2.0-1). libatomic1 set to manually installed. libip4tc2 is already the newest version (1.8.8-1). libip4tc2 set to manually installed. libctf0 is already the newest version (2.38.90.20220713-2). libctf0 set to manually installed. libexpat1 is already the newest version (2.4.8-1). libexpat1 set to manually installed. base-files is already the newest version (12.2). libgdbm-compat4 is already the newest version (1.23-1+b1). libgdbm-compat4 set to manually installed. libx11-data is already the newest version (2:1.8.1-2). libx11-data set to manually installed. libncurses6 is already the newest version (6.3+20220423-2). libncurses6 set to manually installed. libice6 is already the newest version (2:1.0.10-1). libice6 set to manually installed. libfontconfig1 is already the newest version (2.13.1-4.4). libfontconfig1 set to manually installed. libpipeline1 is already the newest version (1.5.6-2). libpipeline1 set to manually installed. gettext is already the newest version (0.21-9). gettext set to manually installed. libc6 is already the newest version (2.34-7). patch is already the newest version (2.7.6-7). patch set to manually installed. po-debconf is already the newest version (1.0.21+nmu1). po-debconf set to manually installed. sensible-utils is already the newest version (0.0.17). sensible-utils set to manually installed. python3-pysam is already the newest version (0.17.0+ds-2+b2). python3-pysam set to manually installed. libtirpc3 is already the newest version (1.3.3+ds-1). libtirpc3 set to manually installed. libzstd1 is already the newest version (1.5.2+dfsg-1). python3-minimal is already the newest version (3.10.6-1). python3-minimal set to manually installed. gettext-base is already the newest version (0.21-9). gettext-base set to manually installed. libgts-0.7-5 is already the newest version (0.7.6+darcs121130-5). libgts-0.7-5 set to manually installed. libxcb-render0 is already the newest version (1.15-1). libxcb-render0 set to manually installed. help2man is already the newest version (1.49.2). help2man set to manually installed. libpython3-stdlib is already the newest version (3.10.6-1). libpython3-stdlib set to manually installed. libxext6 is already the newest version (2:1.3.4-1). libxext6 set to manually installed. coreutils is already the newest version (8.32-4.1). libdpkg-perl is already the newest version (1.21.9). libdpkg-perl set to manually installed. libgomp1 is already the newest version (12.2.0-1). libgomp1 set to manually installed. libldap-2.5-0 is already the newest version (2.5.12+dfsg-2+b1). libldap-2.5-0 set to manually installed. libpam-modules is already the newest version (1.5.2-2). libsasl2-2 is already the newest version (2.1.28+dfsg-7). libsasl2-2 set to manually installed. libgvpr2 is already the newest version (2.42.2-7). libgvpr2 set to manually installed. libhogweed6 is already the newest version (3.8.1-2). libhogweed6 set to manually installed. libpam-modules-bin is already the newest version (1.5.2-2). dpkg is already the newest version (1.21.9). build-essential is already the newest version (12.9). build-essential set to manually installed. ncurses-bin is already the newest version (6.3+20220423-2). libc6-dev is already the newest version (2.34-7). libc6-dev set to manually installed. libssl3 is already the newest version (3.0.5-2). libssl3 set to manually installed. libjpeg62-turbo is already the newest version (1:2.1.2-1). libjpeg62-turbo set to manually installed. init-system-helpers is already the newest version (1.64). gcc is already the newest version (4:12.2.0-1). gcc set to manually installed. sysvinit-utils is already the newest version (3.04-1). libtool is already the newest version (2.4.7-4). libtool set to manually installed. libwebp7 is already the newest version (1.2.2-2+b1). libwebp7 set to manually installed. m4 is already the newest version (1.4.19-1). m4 set to manually installed. libgvc6 is already the newest version (2.42.2-7). libgvc6 set to manually installed. libjbig0 is already the newest version (2.1-3.1+b2). libjbig0 set to manually installed. libtirpc-dev is already the newest version (1.3.3+ds-1). libtirpc-dev set to manually installed. libsparsehash-dev is already the newest version (2.0.3-2). libsparsehash-dev set to manually installed. python3 is already the newest version (3.10.6-1). python3 set to manually installed. libpam-runtime is already the newest version (1.5.2-2). libjson-c5 is already the newest version (0.16-1). libjson-c5 set to manually installed. dh-python is already the newest version (5.20220819). dh-python set to manually installed. libxml2 is already the newest version (2.9.14+dfsg-1+b1). libxml2 set to manually installed. libunistring2 is already the newest version (1.0-1). libunistring2 set to manually installed. librtmp1 is already the newest version (2.4+20151223.gitfa8646d.1-2+b2). librtmp1 set to manually installed. zlib1g-dev is already the newest version (1:1.2.11.dfsg-4.1). zlib1g-dev set to manually installed. libgcc-12-dev is already the newest version (12.2.0-1). libgcc-12-dev set to manually installed. libdevmapper1.02.1 is already the newest version (2:1.02.185-1). libdevmapper1.02.1 set to manually installed. libcgraph6 is already the newest version (2.42.2-7). libcgraph6 set to manually installed. libpixman-1-0 is already the newest version (0.40.0-1). libpixman-1-0 set to manually installed. libgpg-error0 is already the newest version (1.45-2). libdebconfclient0 is already the newest version (0.264). libcap-ng0 is already the newest version (0.8.3-1+b1). automake is already the newest version (1:1.16.5-1.3). automake set to manually installed. libdatrie1 is already the newest version (0.2.13-2). libdatrie1 set to manually installed. libfile-stripnondeterminism-perl is already the newest version (1.13.0-1). libfile-stripnondeterminism-perl set to manually installed. libsasl2-modules-db is already the newest version (2.1.28+dfsg-7). libsasl2-modules-db set to manually installed. python3.10 is already the newest version (3.10.6-1). python3.10 set to manually installed. media-types is already the newest version (8.0.0). media-types set to manually installed. libpangocairo-1.0-0 is already the newest version (1.50.9+ds-1). libpangocairo-1.0-0 set to manually installed. libtiff5 is already the newest version (4.4.0-4). libtiff5 set to manually installed. libtinfo6 is already the newest version (6.3+20220423-2). libxau6 is already the newest version (1:1.0.9-1). libxau6 set to manually installed. libacl1 is already the newest version (2.3.1-1). libseccomp2 is already the newest version (2.5.4-1+b1). libseccomp2 set to manually installed. libgnutls30 is already the newest version (3.7.7-2). libgnutls30 set to manually installed. liblab-gamut1 is already the newest version (2.42.2-7). liblab-gamut1 set to manually installed. dmsetup is already the newest version (2:1.02.185-1). dmsetup set to manually installed. libncursesw6 is already the newest version (6.3+20220423-2). libncursesw6 set to manually installed. libstdc++-12-dev is already the newest version (12.2.0-1). libstdc++-12-dev set to manually installed. libtasn1-6 is already the newest version (4.18.0-4). libtasn1-6 set to manually installed. libnghttp2-14 is already the newest version (1.49.0-1). libnghttp2-14 set to manually installed. libnsl-dev is already the newest version (1.3.0-2). libnsl-dev set to manually installed. systemd is already the newest version (251.4-3). systemd set to manually installed. libuuid1 is already the newest version (2.38.1-1). libbamtools-dev is already the newest version (2.5.2+dfsg-2). libbamtools-dev set to manually installed. libthai-data is already the newest version (0.1.29-1). libthai-data set to manually installed. debconf is already the newest version (1.5.79). libcdt5 is already the newest version (2.42.2-7). libcdt5 set to manually installed. libnettle8 is already the newest version (3.8.1-2). libnettle8 set to manually installed. libperl5.34 is already the newest version (5.34.0-5). libperl5.34 set to manually installed. cpp is already the newest version (4:12.2.0-1). cpp set to manually installed. libhtscodecs2 is already the newest version (1.2.2-1). libhtscodecs2 set to manually installed. graphviz is already the newest version (2.42.2-7). graphviz set to manually installed. libbz2-1.0 is already the newest version (1.0.8-5). libidn2-0 is already the newest version (2.3.3-1+b1). libidn2-0 set to manually installed. libcrypt1 is already the newest version (1:4.4.28-2). libsmartcols1 is already the newest version (2.38.1-1). libgssapi-krb5-2 is already the newest version (1.20-1). libgssapi-krb5-2 set to manually installed. g++ is already the newest version (4:12.2.0-1). g++ set to manually installed. libargon2-1 is already the newest version (0~20171227-0.3). libargon2-1 set to manually installed. libfdisk1 is already the newest version (2.38.1-1). libfdisk1 set to manually installed. debhelper is already the newest version (13.9.1). debhelper set to manually installed. libltdl7 is already the newest version (2.4.7-4). libltdl7 set to manually installed. libtirpc-common is already the newest version (1.3.3+ds-1). libtirpc-common set to manually installed. libpcre2-8-0 is already the newest version (10.40-1). dh-strip-nondeterminism is already the newest version (1.13.0-1). dh-strip-nondeterminism set to manually installed. perl-base is already the newest version (5.34.0-5). groff-base is already the newest version (1.22.4-8). groff-base set to manually installed. gzip is already the newest version (1.12-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg -r debootsnap-dummy' exec /srv/rebuilderd/tmp/mmdebstrap.tII8zHIu_F (Reading database ... 14905 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.tII8zHIu_F I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.tII8zHIu_F I: running special hook: upload sources.list /etc/apt/sources.list I: waiting for background processes to finish... I: cleaning package lists and apt cache... I: skipping cleanup/reproducible as requested I: creating tarball... I: done I: removing tempdir /srv/rebuilderd/tmp/mmdebstrap.tII8zHIu_F... I: success in 55.6421 seconds Downloading dependency 135 of 255: binutils:armel=2.38.90.20220713-2 Downloading dependency 136 of 255: libicu71:armel=71.1-3 Downloading dependency 137 of 255: libubsan1:armel=12.2.0-1 Downloading dependency 138 of 255: libpcre3:armel=2:8.39-14 Downloading dependency 139 of 255: libsm6:armel=2:1.2.3-1 Downloading dependency 140 of 255: lsb-base:armel=11.2 Downloading dependency 141 of 255: libreadline8:armel=8.2~rc2-2 Downloading dependency 142 of 255: debianutils:armel=5.7-0.3 Downloading dependency 143 of 255: libatomic1:armel=12.2.0-1 Downloading dependency 144 of 255: libip4tc2:armel=1.8.8-1 Downloading dependency 145 of 255: libctf0:armel=2.38.90.20220713-2 Downloading dependency 146 of 255: libexpat1:armel=2.4.8-1 Downloading dependency 147 of 255: base-files:armel=12.2 Downloading dependency 148 of 255: libgdbm-compat4:armel=1.23-1+b1 Downloading dependency 149 of 255: libx11-data:armel=2:1.8.1-2 Downloading dependency 150 of 255: 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255: libssl3:armel=3.0.5-2 Downloading dependency 183 of 255: libjpeg62-turbo:armel=1:2.1.2-1 Downloading dependency 184 of 255: init-system-helpers:armel=1.64 Downloading dependency 185 of 255: gcc:armel=4:12.2.0-1 Downloading dependency 186 of 255: sysvinit-utils:armel=3.04-1 Downloading dependency 187 of 255: libtool:armel=2.4.7-4 Downloading dependency 188 of 255: libwebp7:armel=1.2.2-2+b1 Downloading dependency 189 of 255: m4:armel=1.4.19-1 Downloading dependency 190 of 255: libgvc6:armel=2.42.2-7 Downloading dependency 191 of 255: libjbig0:armel=2.1-3.1+b2 Downloading dependency 192 of 255: libtirpc-dev:armel=1.3.3+ds-1 Downloading dependency 193 of 255: libsparsehash-dev:armel=2.0.3-2 Downloading dependency 194 of 255: python3:armel=3.10.6-1 Downloading dependency 195 of 255: libpam-runtime:armel=1.5.2-2 Downloading dependency 196 of 255: libjson-c5:armel=0.16-1 Downloading dependency 197 of 255: dh-python:armel=5.20220819 Downloading dependency 198 of 255: libxml2:armel=2.9.14+dfsg-1+b1 Downloading dependency 199 of 255: libunistring2:armel=1.0-1 Downloading dependency 200 of 255: librtmp1:armel=2.4+20151223.gitfa8646d.1-2+b2 Downloading dependency 201 of 255: zlib1g-dev:armel=1:1.2.11.dfsg-4.1 Downloading dependency 202 of 255: libgcc-12-dev:armel=12.2.0-1 Downloading dependency 203 of 255: libdevmapper1.02.1:armel=2:1.02.185-1 Downloading dependency 204 of 255: libcgraph6:armel=2.42.2-7 Downloading dependency 205 of 255: libpixman-1-0:armel=0.40.0-1 Downloading dependency 206 of 255: libgpg-error0:armel=1.45-2 Downloading dependency 207 of 255: libdebconfclient0:armel=0.264 Downloading dependency 208 of 255: libcap-ng0:armel=0.8.3-1+b1 Downloading dependency 209 of 255: automake:armel=1:1.16.5-1.3 Downloading dependency 210 of 255: libdatrie1:armel=0.2.13-2 Downloading dependency 211 of 255: libfile-stripnondeterminism-perl:armel=1.13.0-1 Downloading dependency 212 of 255: libsasl2-modules-db:armel=2.1.28+dfsg-7 Downloading dependency 213 of 255: python3.10:armel=3.10.6-1 Downloading dependency 214 of 255: media-types:armel=8.0.0 Downloading dependency 215 of 255: libpangocairo-1.0-0:armel=1.50.9+ds-1 Downloading dependency 216 of 255: libtiff5:armel=4.4.0-4 Downloading dependency 217 of 255: libtinfo6:armel=6.3+20220423-2 Downloading dependency 218 of 255: libxau6:armel=1:1.0.9-1 Downloading dependency 219 of 255: libacl1:armel=2.3.1-1 Downloading dependency 220 of 255: libseccomp2:armel=2.5.4-1+b1 Downloading dependency 221 of 255: libgnutls30:armel=3.7.7-2 Downloading dependency 222 of 255: liblab-gamut1:armel=2.42.2-7 Downloading dependency 223 of 255: dmsetup:armel=2:1.02.185-1 Downloading dependency 224 of 255: libncursesw6:armel=6.3+20220423-2 Downloading dependency 225 of 255: libstdc++-12-dev:armel=12.2.0-1 Downloading dependency 226 of 255: libtasn1-6:armel=4.18.0-4 Downloading dependency 227 of 255: libnghttp2-14:armel=1.49.0-1 Downloading dependency 228 of 255: libnsl-dev:armel=1.3.0-2 Downloading dependency 229 of 255: systemd:armel=251.4-3 Downloading dependency 230 of 255: libuuid1:armel=2.38.1-1 Downloading dependency 231 of 255: libbamtools-dev:armel=2.5.2+dfsg-2 Downloading dependency 232 of 255: libthai-data:armel=0.1.29-1 Downloading dependency 233 of 255: debconf:armel=1.5.79 Downloading dependency 234 of 255: libcdt5:armel=2.42.2-7 Downloading dependency 235 of 255: libnettle8:armel=3.8.1-2 Downloading dependency 236 of 255: libperl5.34:armel=5.34.0-5 Downloading dependency 237 of 255: cpp:armel=4:12.2.0-1 Downloading dependency 238 of 255: libhtscodecs2:armel=1.2.2-1 Downloading dependency 239 of 255: graphviz:armel=2.42.2-7 Downloading dependency 240 of 255: libbz2-1.0:armel=1.0.8-5 Downloading dependency 241 of 255: libidn2-0:armel=2.3.3-1+b1 Downloading dependency 242 of 255: libcrypt1:armel=1:4.4.28-2 Downloading dependency 243 of 255: libsmartcols1:armel=2.38.1-1 Downloading dependency 244 of 255: libgssapi-krb5-2:armel=1.20-1 Downloading dependency 245 of 255: g++:armel=4:12.2.0-1 Downloading dependency 246 of 255: libargon2-1:armel=0~20171227-0.3 Downloading dependency 247 of 255: libfdisk1:armel=2.38.1-1 Downloading dependency 248 of 255: debhelper:armel=13.9.1 Downloading dependency 249 of 255: libltdl7:armel=2.4.7-4 Downloading dependency 250 of 255: libtirpc-common:armel=1.3.3+ds-1 Downloading dependency 251 of 255: libpcre2-8-0:armel=10.40-1 Downloading dependency 252 of 255: dh-strip-nondeterminism:armel=1.13.0-1 Downloading dependency 253 of 255: perl-base:armel=5.34.0-5 Downloading dependency 254 of 255: groff-base:armel=1.22.4-8 Downloading dependency 255 of 255: gzip:armel=1.12-1 env --chdir=/srv/rebuilderd/tmp/rebuilderdR7kwFT/out DEB_BUILD_OPTIONS=parallel=4 LC_ALL=C.UTF-8 SOURCE_DATE_EPOCH=1662152175 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildbRsLVA/debrebuild.sbuildrc.Md7qg8fdOmLd sbuild --build=armel --host=armel --no-source --arch-any --no-arch-all --binNMU-changelog= sga (0.10.15-7+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for armel; no source changes. * Rebuild against libbamtools2.5.2 -- armel Build Daemon (henze) Fri, 02 Sep 2022 20:56:15 +0000 --chroot=/srv/rebuilderd/tmp/debrebuildbRsLVA/debrebuild.tar.ts5tdDBkrRQc --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/sga-qoWx2H --dsc-dir=sga-0.10.15 /srv/rebuilderd/tmp/rebuilderdR7kwFT/inputs/sga_0.10.15-7.dsc I: consider moving your ~/.sbuildrc to /srv/rebuilderd/.config/sbuild/config.pl The Debian buildds switched to the "unshare" backend and sbuild will default to it in the future. To start using "unshare" add this to your `~/.config/sbuild/config.pl`: $chroot_mode = "unshare"; If you want to keep the old "schroot" mode even in the future, add the following to your `~/.config/sbuild/config.pl`: $chroot_mode = "schroot"; $schroot = "schroot"; sbuild: warning: descr(l1): found blank line where expected first heading sbuild (Debian sbuild) 0.89.3 (07 June 2025) on codethink05-arm64 +==============================================================================+ | sga 0.10.15-7+b1 (armel) Mon, 28 Jul 2025 22:58:43 +0000 | +==============================================================================+ Package: sga Version: 0.10.15-7+b1 Source Version: 0.10.15-7 Distribution: unstable Machine Architecture: arm64 Host Architecture: armel Build Architecture: armel Build Type: any I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/rebuilderd/tmp/debrebuildbRsLVA/debrebuild.tar.ts5tdDBkrRQc to /srv/rebuilderd/tmp/tmp.sbuild.ure3MhoPae... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Mon, 28 Jul 2025 22:58:48 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdR7kwFT/inputs/sga_0.10.15-7.dsc exists in /srv/rebuilderd/tmp/rebuilderdR7kwFT/inputs; copying to chroot sbuild: warning: descr(l1): found blank line where expected first heading +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 28 Jul 2025 22:58:51 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, libsparsehash-dev, zlib1g-dev | libz-dev, libbamtools-dev, help2man, samtools, python3, python3-ruffus, python3-pysam, build-essential Filtered Build-Depends: debhelper-compat (= 13), dh-python, libsparsehash-dev, zlib1g-dev, libbamtools-dev, help2man, samtools, python3, python3-ruffus, python3-pysam, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/sga-qoWx2H/resolver-mpACLK/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Mon, 28 Jul 2025 22:58:56 +0000 | +------------------------------------------------------------------------------+ Arch check ok (armel included in any) +------------------------------------------------------------------------------+ | Build environment Mon, 28 Jul 2025 22:58:57 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.38+deb13-cloud-arm64 #1 SMP Debian 6.12.38-1 (2025-07-16) arm64 (aarch64) Toolchain package versions: binutils_2.38.90.20220713-2 dpkg-dev_1.21.9 g++-12_12.2.0-1 gcc-12_12.2.0-1 libc6-dev_2.34-7 libstdc++-12-dev_12.2.0-1 libstdc++6_12.2.0-1 linux-libc-dev_5.18.16-1 Package versions: autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.2 base-passwd_3.6.0 bash_5.2~rc2-2 binutils_2.38.90.20220713-2 binutils-arm-linux-gnueabi_2.38.90.20220713-2 binutils-common_2.38.90.20220713-2 bsdextrautils_2.38.1-1 bsdutils_1:2.38.1-1 build-essential_12.9 bzip2_1.0.8-5 coreutils_8.32-4.1 cpp_4:12.2.0-1 cpp-12_12.2.0-1 dash_0.5.11+git20210903+057cd650a4ed-8 debconf_1.5.79 debhelper_13.9.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-python_5.20220819 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dmsetup_2:1.02.185-1 dpkg_1.21.9 dpkg-dev_1.21.9 dwz_0.14-1 file_1:5.41-4 findutils_4.9.0-3 fontconfig_2.13.1-4.4 fontconfig-config_2.13.1-4.4 fonts-dejavu-core_2.37-2 g++_4:12.2.0-1 g++-12_12.2.0-1 gcc_4:12.2.0-1 gcc-12_12.2.0-1 gcc-12-base_12.2.0-1 gettext_0.21-9 gettext-base_0.21-9 graphviz_2.42.2-7 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 help2man_1.49.2 hostname_3.23 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapparmor1_3.0.7-1 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan8_12.2.0-1 libatomic1_12.2.0-1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1+b1 libbamtools-dev_2.5.2+dfsg-2 libbamtools2.5.2_2.5.2+dfsg-2 libbinutils_2.38.90.20220713-2 libblkid1_2.38.1-1 libbrotli1_1.0.9-2+b4 libbsd0_0.11.6-1 libbz2-1.0_1.0.8-5 libc-bin_2.34-7 libc-dev-bin_2.34-7 libc6_2.34-7 libc6-dev_2.34-7 libcairo2_1.16.0-6 libcap-ng0_0.8.3-1+b1 libcap2_1:2.44-1 libcc1-0_12.2.0-1 libcdt5_2.42.2-7 libcgraph6_2.42.2-7 libcom-err2_1.46.5-2 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libcryptsetup12_2:2.5.0-2 libctf-nobfd0_2.38.90.20220713-2 libctf0_2.38.90.20220713-2 libcurl3-gnutls_7.85.0-1 libdatrie1_0.2.13-2 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.9.1 libdeflate0_1.12-1 libdevmapper1.02.1_2:1.02.185-1 libdpkg-perl_1.21.9 libelf1_0.187-1 libexpat1_2.4.8-1 libfdisk1_2.38.1-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libfontconfig1_2.13.1-4.4 libfreetype6_2.12.1+dfsg-3 libfribidi0_1.0.8-2.1 libgcc-12-dev_12.2.0-1 libgcc-s1_12.2.0-1 libgcrypt20_1.10.1-2 libgd3_2.3.3-6 libgdbm-compat4_1.23-1+b1 libgdbm6_1.23-1+b1 libglib2.0-0_2.73.3-3 libgmp10_2:6.2.1+dfsg1-1 libgnutls30_3.7.7-2 libgomp1_12.2.0-1 libgpg-error0_1.45-2 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.20-1 libgts-0.7-5_0.7.6+darcs121130-5 libgvc6_2.42.2-7 libgvpr2_2.42.2-7 libharfbuzz0b_2.7.4-1+b1 libhogweed6_3.8.1-2 libhts3_1.13+ds-2+b1 libhtscodecs2_1.2.2-1 libice6_2:1.0.10-1 libicu71_71.1-3 libidn2-0_2.3.3-1+b1 libip4tc2_1.8.8-1 libisl23_0.25-1 libjbig0_2.1-3.1+b2 libjpeg62-turbo_1:2.1.2-1 libjson-c5_0.16-1 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkmod2_30+20220630-3 libkrb5-3_1.20-1 libkrb5support0_1.20-1 liblab-gamut1_2.42.2-7 libldap-2.5-0_2.5.12+dfsg-2+b1 liblerc4_4.0.0+ds-1 liblocale-gettext-perl_1.07-4+b2 libltdl7_2.4.7-4 liblz4-1_1.9.4-1 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmount1_2.38.1-1 libmpc3_1.2.1-2 libmpdec3_2.5.1-2 libmpfr6_4.1.0-3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnghttp2-14_1.49.0-1 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-modules_1.5.2-2 libpam-modules-bin_1.5.2-2 libpam-runtime_1.5.2-2 libpam0g_1.5.2-2 libpango-1.0-0_1.50.9+ds-1 libpangocairo-1.0-0_1.50.9+ds-1 libpangoft2-1.0-0_1.50.9+ds-1 libpathplan4_2.42.2-7 libpcre2-8-0_10.40-1 libpcre3_2:8.39-14 libperl5.34_5.34.0-5 libpipeline1_1.5.6-2 libpixman-1-0_0.40.0-1 libpng16-16_1.6.37-5 libpsl5_0.21.0-1.2 libpython3-stdlib_3.10.6-1 libpython3.10-minimal_3.10.6-1 libpython3.10-stdlib_3.10.6-1 libreadline8_8.2~rc2-2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-7 libsasl2-modules-db_2.1.28+dfsg-7 libseccomp2_2.5.4-1+b1 libselinux1_3.4-1+b1 libsm6_2:1.2.3-1 libsmartcols1_2.38.1-1 libsparsehash-dev_2.0.3-2 libsqlite3-0_3.39.2-1 libssh2-1_1.10.0-3+b1 libssl3_3.0.5-2 libstdc++-12-dev_12.2.0-1 libstdc++6_12.2.0-1 libsub-override-perl_0.09-3 libsystemd-shared_251.4-3 libsystemd0_251.4-3 libtasn1-6_4.18.0-4 libthai-data_0.1.29-1 libthai0_0.1.29-1 libtiff5_4.4.0-4 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libubsan1_12.2.0-1 libuchardet0_0.0.7-1 libudev1_251.4-3 libunistring2_1.0-1 libuuid1_2.38.1-1 libwebp7_1.2.2-2+b1 libx11-6_2:1.8.1-2 libx11-data_2:1.8.1-2 libxau6_1:1.0.9-1 libxaw7_2:1.0.14-1 libxcb-render0_1.15-1 libxcb-shm0_1.15-1 libxcb1_1.15-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxml2_2.9.14+dfsg-1+b1 libxmu6_2:1.1.3-3 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1.1 libxt6_1:1.2.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.18.16-1 login_1:4.11.1+dfsg1-2 lsb-base_11.2 m4_1.4.19-1 make_4.3-4.1 man-db_2.10.2-2 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38.1-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 patch_2.7.6-7 perl_5.34.0-5 perl-base_5.34.0-5 perl-modules-5.34_5.34.0-5 po-debconf_1.0.21+nmu1 python3_3.10.6-1 python3-distutils_3.10.6-1 python3-lib2to3_3.10.6-1 python3-minimal_3.10.6-1 python3-pysam_0.17.0+ds-2+b2 python3-ruffus_2.8.4-4 python3.10_3.10.6-1 python3.10-minimal_3.10.6-1 readline-common_8.2~rc2-2 rpcsvc-proto_1.4.2-4 samtools_1.13-4 sed_4.8-1 sensible-utils_0.0.17 systemd_251.4-3 sysvinit-utils_3.04-1 tar_1.34+dfsg-1 ucf_3.0043 util-linux_2.38.1-1 util-linux-extra_2.38.1-1 x11-common_1:7.7+23 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1 +------------------------------------------------------------------------------+ | Build Mon, 28 Jul 2025 22:58:57 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: sga Binary: sga Architecture: any Version: 0.10.15-7 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille Homepage: https://github.com/jts/sga Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/sga Vcs-Git: https://salsa.debian.org/med-team/sga.git Build-Depends: debhelper-compat (= 13), dh-python, libsparsehash-dev, zlib1g-dev | libz-dev, libbamtools-dev, help2man, samtools , python3 , python3-ruffus , python3-pysam Package-List: sga deb science optional arch=any Checksums-Sha1: 55b540d2f1cae3a44de8da6db8f413826bdb5f14 6569986 sga_0.10.15.orig.tar.gz 4598b0bf58446b932f202a8bfa7e9d9d3bc018de 214356 sga_0.10.15-7.debian.tar.xz Checksums-Sha256: 1b18996e6ec47985bc4889a8cbc3cd4dd3a8c7d385ae9f450bd474e36342558b 6569986 sga_0.10.15.orig.tar.gz 708c923249099329004802eb6fe1b549b6421e5d3cf10d81c624db65e381117f 214356 sga_0.10.15-7.debian.tar.xz Files: 990aed1593f8072650c6366e5cf32519 6569986 sga_0.10.15.orig.tar.gz 420c1f46b48f89950ac7e500402215e8 214356 sga_0.10.15-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmFEoJwACgkQPCZ2P2xn 5uIThw/5AcAmhXJYwdZ93J6fhmzcEOSTkqi8GdH/9Nlt3BCVIZlJR3/6vcttoVUo sKob/Rr78LGESV215LOC13J9soUrZa6giB6aM+wU+hVhD81dCt7zz2bsMSvwopC8 DNmWt3cZta4xDM7MxuBL5cztJZThE8ewwbZ3VQmGHix/aAMOlcK2EsP9iQCpRepF Ovmc4kDe1USc6erpE3cohGVlHfoJy4JXggHjvKqHz4u4YGFLQNpHpT70LH9HSrgh thqrPnnI9I2CjNxF2WSYIFMCD5f1Iq9TWihNi4H6m0keRgZcFE1lKjKuP8WYT9rK GLvaAGaLC1sB0BZ0lLpf18pySxNUzA/EtX6RzBes0UMRG9SkWG2lOFTyZRJjhC/3 Mz3FGKLROVKjTOerTgdhDKCoAPa/VLwXIYZLX/xxHxVelJibqPHRlWuS6xaJkunW OzPueUfUSynrS9kQZ5bM0CIfmhl+9zqWKNIfvwRDqmTh5meaH/oYneMgUIKSJgLa PBU8/Qc+FzpObFe71EIRa/5vs+kUQcvLIoeFqYMoDLd5WFwyFlTTe035u4SKpA7q EOADJZbbLzqBP89tgkWjglsUCVClDBUeyuocQXREI85kW9GkoWnwvKqkZaRNncxO UdqDEwW4NwADMhzii6hdLiJxBiYBhcLkP+ciz4TxX2wUKU6qO1U= =KU9x -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify signature on ./sga_0.10.15-7.dsc since GnuPG is not installed dpkg-source: info: extracting sga in /build/sga-qoWx2H/sga-0.10.15 dpkg-source: info: unpacking sga_0.10.15.orig.tar.gz dpkg-source: info: unpacking sga_0.10.15-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0002-no-rpath.patch dpkg-source: info: applying 0003-do-not-dist-unsup-script.patch dpkg-source: info: applying 0004-Add-help-to-sga-bam2de.pl.patch dpkg-source: info: applying 0005-Remove-extensions-on-scripts-we-ship.patch dpkg-source: info: applying 0006-remove-google-addsense.patch dpkg-source: info: applying gcc-7.patch dpkg-source: info: applying no_privacy_breach_url.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying no_enforcing_c++98.patch dpkg-source: info: applying gcc9.patch Install fakeroot ---------------- Setup apt archive ----------------- Merged Build-Depends: fakeroot Filtered Build-Depends: fakeroot dpkg-deb: building package 'sbuild-build-depends-fakeroot-dummy' in '/build/sga-qoWx2H/resolver-mpACLK/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 Hack binNMU version ------------------- Created changelog entry for binNMU version 0.10.15-7+b1 +------------------------------------------------------------------------------+ | Starting Timed Build Commands Mon, 28 Jul 2025 22:59:03 +0000 | +------------------------------------------------------------------------------+ grep -iq "^Rules-Requires-Root:" "/build/sga-qoWx2H/sga-0.10.15/debian/control" || sed -i "1iRules-Requires-Root: no" "/build/sga-qoWx2H/sga-0.10.15/debian/control" -------------------------------------------------------------------------------------------------------------------------------------------------------------------- I: Finished running 'grep -iq "^Rules-Requires-Root:" "/build/sga-qoWx2H/sga-0.10.15/debian/control" || sed -i "1iRules-Requires-Root: no" "/build/sga-qoWx2H/sga-0.10.15/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 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh SOURCE_DATE_EPOCH=1662152175 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -B dpkg-buildpackage: info: source package sga dpkg-buildpackage: info: source version 0.10.15-7+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by armel Build Daemon (henze) dpkg-source --before-build . dpkg-buildpackage: info: host architecture armel debian/rules clean dh clean --with python3 --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary-arch dh binary-arch --with python3 --sourcedirectory=src dh_update_autotools_config -a -O--sourcedirectory=src dh_autoreconf -a -O--sourcedirectory=src configure.ac:7: warning: The macro `AC_CONFIG_HEADER' is obsolete. configure.ac:7: You should run autoupdate. ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from... configure.ac:7: the top level configure.ac:24: warning: The macro `AC_TRY_LINK' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... m4/m4_ax_openmp.m4:70: AX_OPENMP is expanded from... configure.ac:24: the top level configure.ac:12: installing './compile' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' Algorithm/Makefile.am: installing './depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/sga-qoWx2H/sga-0.10.15' dh_auto_configure -- --with-bamtools=/usr/ cd src && ./configure --build=arm-linux-gnueabi --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabi --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-bamtools=/usr/ checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for ranlib... ranlib checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for zlib.h... yes checking for library containing gzopen... -lz checking for library containing clock_gettime... none required checking for OpenMP flag of C++ compiler... -fopenmp checking for host type... you are not using osx so multi-threading should work. checking for google/sparse_hash_set... yes checking for google/sparse_hash_set... (cached) yes checking for google/sparse_hash_map... yes checking for unordered_map... yes checking for tr1/unordered_map... yes checking for ext/hash_map... yes checking for unordered_set... yes checking for tr1/unordered_set... yes checking for ext/hash_set... yes checking for api/BamReader.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating bin/Makefile config.status: creating Thirdparty/Makefile config.status: creating Util/Makefile config.status: creating SQG/Makefile config.status: creating Bigraph/Makefile config.status: creating Algorithm/Makefile config.status: creating StringGraph/Makefile config.status: creating Concurrency/Makefile config.status: creating SuffixTools/Makefile config.status: creating GraphDiff/Makefile config.status: creating Scaffold/Makefile config.status: creating SGA/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15' dh_auto_build -a -O--sourcedirectory=src cd src && make -j4 make[1]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src' make all-recursive make[2]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src' Making all in bin make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/bin' cp -n sga-bam2de.pl sga-bam2de cp -n sga-mergeDriver.pl sga-mergeDriver make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/bin' Making all in Thirdparty make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Thirdparty' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gzstream.o gzstream.C gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -std=gnu99 -O3 -c -o stdaln.o stdaln.c g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o overlapper.o overlapper.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o multiple_alignment.o multiple_alignment.cpp overlapper.cpp:37:64: warning: missing initializer for member ‘OverlapperParams::gap_s1_start’ [-Wmissing-field-initializers] 37 | OverlapperParams default_params = { 2, -6, -3, -2, ALT_OVERLAP }; | ^ overlapper.cpp:37:64: warning: missing initializer for member ‘OverlapperParams::gap_s1_end’ [-Wmissing-field-initializers] overlapper.cpp:37:64: warning: missing initializer for member ‘OverlapperParams::gap_s2_start’ [-Wmissing-field-initializers] overlapper.cpp:37:64: warning: missing initializer for member ‘OverlapperParams::gap_s2_end’ [-Wmissing-field-initializers] overlapper.cpp:37:64: warning: missing initializer for member ‘OverlapperParams::use_m_ops’ [-Wmissing-field-initializers] overlapper.cpp:38:69: warning: missing initializer for member ‘OverlapperParams::gap_s1_start’ [-Wmissing-field-initializers] 38 | OverlapperParams ungapped_params = { 2, -10000, -3, -2, ALT_OVERLAP }; | ^ overlapper.cpp:38:69: warning: missing initializer for member ‘OverlapperParams::gap_s1_end’ [-Wmissing-field-initializers] overlapper.cpp:38:69: warning: missing initializer for member ‘OverlapperParams::gap_s2_start’ [-Wmissing-field-initializers] overlapper.cpp:38:69: warning: missing initializer for member ‘OverlapperParams::gap_s2_end’ [-Wmissing-field-initializers] overlapper.cpp:38:69: warning: missing initializer for member ‘OverlapperParams::use_m_ops’ [-Wmissing-field-initializers] stdaln.c: In function ‘aln_local_core’: stdaln.c:756:17: warning: ‘free’ called on pointer ‘*(int **)((char *)(void *) ivtmp.728_209)’ with nonzero offset 4 [-Wfree-nonheap-object] 756 | free(s_array[i]); | ^~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -std=gnu99 -O3 -c -o bcr.o bcr.c bcr.c: In function ‘ld_restore’: bcr.c:183:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 183 | fread(&ld->max, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bcr.c:186:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 186 | fread(&x, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bcr.c:189:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 189 | fread(ld->a[i], 8, x, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MurmurHash3.o MurmurHash3.cpp MurmurHash3.cpp: In function ‘void MurmurHash3_x86_32(const void*, int, uint32_t, void*)’: MurmurHash3.cpp:132:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 132 | case 3: k1 ^= tail[2] << 16; | ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:133:3: note: here 133 | case 2: k1 ^= tail[1] << 8; | ^~~~ MurmurHash3.cpp:133:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 133 | case 2: k1 ^= tail[1] << 8; | ~~~^~~~~~~~~~~~~~~ MurmurHash3.cpp:134:3: note: here 134 | case 1: k1 ^= tail[0]; | ^~~~ MurmurHash3.cpp: In function ‘void MurmurHash3_x86_128(const void*, int, uint32_t, void*)’: MurmurHash3.cpp:207:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 207 | case 15: k4 ^= tail[14] << 16; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:208:3: note: here 208 | case 14: k4 ^= tail[13] << 8; | ^~~~ MurmurHash3.cpp:208:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 208 | case 14: k4 ^= tail[13] << 8; | ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:209:3: note: here 209 | case 13: k4 ^= tail[12] << 0; | ^~~~ MurmurHash3.cpp:210:56: warning: this statement may fall through [-Wimplicit-fallthrough=] 210 | k4 *= c4; k4 = ROTL32(k4,18); k4 *= c1; h4 ^= k4; | ~~~^~~~~ MurmurHash3.cpp:212:3: note: here 212 | case 12: k3 ^= tail[11] << 24; | ^~~~ MurmurHash3.cpp:212:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 212 | case 12: k3 ^= tail[11] << 24; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:213:3: note: here 213 | case 11: k3 ^= tail[10] << 16; | ^~~~ MurmurHash3.cpp:213:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 213 | case 11: k3 ^= tail[10] << 16; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:214:3: note: here 214 | case 10: k3 ^= tail[ 9] << 8; | ^~~~ MurmurHash3.cpp:214:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 214 | case 10: k3 ^= tail[ 9] << 8; | ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:215:3: note: here 215 | case 9: k3 ^= tail[ 8] << 0; | ^~~~ MurmurHash3.cpp:216:56: warning: this statement may fall through [-Wimplicit-fallthrough=] 216 | k3 *= c3; k3 = ROTL32(k3,17); k3 *= c4; h3 ^= k3; | ~~~^~~~~ MurmurHash3.cpp:218:3: note: here 218 | case 8: k2 ^= tail[ 7] << 24; | ^~~~ MurmurHash3.cpp:218:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 218 | case 8: k2 ^= tail[ 7] << 24; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:219:3: note: here 219 | case 7: k2 ^= tail[ 6] << 16; | ^~~~ MurmurHash3.cpp:219:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 219 | case 7: k2 ^= tail[ 6] << 16; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:220:3: note: here 220 | case 6: k2 ^= tail[ 5] << 8; | ^~~~ MurmurHash3.cpp:220:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 220 | case 6: k2 ^= tail[ 5] << 8; | ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:221:3: note: here 221 | case 5: k2 ^= tail[ 4] << 0; | ^~~~ MurmurHash3.cpp:222:56: warning: this statement may fall through [-Wimplicit-fallthrough=] 222 | k2 *= c2; k2 = ROTL32(k2,16); k2 *= c3; h2 ^= k2; | ~~~^~~~~ MurmurHash3.cpp:224:3: note: here 224 | case 4: k1 ^= tail[ 3] << 24; | ^~~~ MurmurHash3.cpp:224:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 224 | case 4: k1 ^= tail[ 3] << 24; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:225:3: note: here 225 | case 3: k1 ^= tail[ 2] << 16; | ^~~~ MurmurHash3.cpp:225:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 225 | case 3: k1 ^= tail[ 2] << 16; | ~~~^~~~~~~~~~~~~~~~~ MurmurHash3.cpp:226:3: note: here 226 | case 2: k1 ^= tail[ 1] << 8; | ^~~~ MurmurHash3.cpp:226:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 226 | case 2: k1 ^= tail[ 1] << 8; | ~~~^~~~~~~~~~~~~~~~ MurmurHash3.cpp:227:3: note: here 227 | case 1: k1 ^= tail[ 0] << 0; | ^~~~ MurmurHash3.cpp: In function ‘void MurmurHash3_x64_128(const void*, int, uint32_t, void*)’: MurmurHash3.cpp:296:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 296 | case 15: k2 ^= uint64_t(tail[14]) << 48; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:297:3: note: here 297 | case 14: k2 ^= uint64_t(tail[13]) << 40; | ^~~~ MurmurHash3.cpp:297:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 297 | case 14: k2 ^= uint64_t(tail[13]) << 40; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:298:3: note: here 298 | case 13: k2 ^= uint64_t(tail[12]) << 32; | ^~~~ MurmurHash3.cpp:298:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 298 | case 13: k2 ^= uint64_t(tail[12]) << 32; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:299:3: note: here 299 | case 12: k2 ^= uint64_t(tail[11]) << 24; | ^~~~ MurmurHash3.cpp:299:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 299 | case 12: k2 ^= uint64_t(tail[11]) << 24; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:300:3: note: here 300 | case 11: k2 ^= uint64_t(tail[10]) << 16; | ^~~~ MurmurHash3.cpp:300:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 300 | case 11: k2 ^= uint64_t(tail[10]) << 16; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:301:3: note: here 301 | case 10: k2 ^= uint64_t(tail[ 9]) << 8; | ^~~~ MurmurHash3.cpp:301:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 301 | case 10: k2 ^= uint64_t(tail[ 9]) << 8; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:302:3: note: here 302 | case 9: k2 ^= uint64_t(tail[ 8]) << 0; | ^~~~ MurmurHash3.cpp:303:56: warning: this statement may fall through [-Wimplicit-fallthrough=] 303 | k2 *= c2; k2 = ROTL64(k2,33); k2 *= c1; h2 ^= k2; | ~~~^~~~~ MurmurHash3.cpp:305:3: note: here 305 | case 8: k1 ^= uint64_t(tail[ 7]) << 56; | ^~~~ MurmurHash3.cpp:305:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 305 | case 8: k1 ^= uint64_t(tail[ 7]) << 56; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:306:3: note: here 306 | case 7: k1 ^= uint64_t(tail[ 6]) << 48; | ^~~~ MurmurHash3.cpp:306:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 306 | case 7: k1 ^= uint64_t(tail[ 6]) << 48; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:307:3: note: here 307 | case 6: k1 ^= uint64_t(tail[ 5]) << 40; | ^~~~ MurmurHash3.cpp:307:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 307 | case 6: k1 ^= uint64_t(tail[ 5]) << 40; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:308:3: note: here 308 | case 5: k1 ^= uint64_t(tail[ 4]) << 32; | ^~~~ MurmurHash3.cpp:308:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 308 | case 5: k1 ^= uint64_t(tail[ 4]) << 32; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:309:3: note: here 309 | case 4: k1 ^= uint64_t(tail[ 3]) << 24; | ^~~~ MurmurHash3.cpp:309:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 309 | case 4: k1 ^= uint64_t(tail[ 3]) << 24; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:310:3: note: here 310 | case 3: k1 ^= uint64_t(tail[ 2]) << 16; | ^~~~ MurmurHash3.cpp:310:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 310 | case 3: k1 ^= uint64_t(tail[ 2]) << 16; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:311:3: note: here 311 | case 2: k1 ^= uint64_t(tail[ 1]) << 8; | ^~~~ MurmurHash3.cpp:311:15: warning: this statement may fall through [-Wimplicit-fallthrough=] 311 | case 2: k1 ^= uint64_t(tail[ 1]) << 8; | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ MurmurHash3.cpp:312:3: note: here 312 | case 1: k1 ^= uint64_t(tail[ 0]) << 0; | ^~~~ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o count_min_sketch.o count_min_sketch.cpp rm -f libthirdparty.a ar cru libthirdparty.a gzstream.o stdaln.o overlapper.o multiple_alignment.o bcr.o MurmurHash3.o count_min_sketch.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libthirdparty.a make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Thirdparty' Making all in Util make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Util' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Util.o `test -f 'Util.cpp' || echo './'`Util.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Alphabet.o `test -f 'Alphabet.cpp' || echo './'`Alphabet.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Contig.o `test -f 'Contig.cpp' || echo './'`Contig.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-ReadTable.o `test -f 'ReadTable.cpp' || echo './'`ReadTable.cpp Alphabet.cpp:101:84: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 101 | template<> const size_t AlphaCount64::maxValue = std::numeric_limits::max(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-ReadInfoTable.o `test -f 'ReadInfoTable.cpp' || echo './'`ReadInfoTable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-SeqReader.o `test -f 'SeqReader.cpp' || echo './'`SeqReader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-DNAString.o `test -f 'DNAString.cpp' || echo './'`DNAString.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Match.o `test -f 'Match.cpp' || echo './'`Match.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Pileup.o `test -f 'Pileup.cpp' || echo './'`Pileup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-BitChar.o `test -f 'BitChar.cpp' || echo './'`BitChar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Interval.o `test -f 'Interval.cpp' || echo './'`Interval.cpp In file included from Pileup.h:12, from Pileup.cpp:10: Pileup.cpp: In member function ‘DNADouble Pileup::calculateSimpleAlphaProb() const’: Util.h:32:53: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \ | ^~ Pileup.cpp:46:5: note: in expansion of macro ‘WARN_ONCE’ 46 | WARN_ONCE("Fix Pileup::calculateSimpleDNADouble numerical stability"); | ^~~~~~~~~ Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 33 | printf("WARNING: [%s]\n", (x)); _warn_once = false; | ^~~~~~~~~~ Pileup.cpp:46:5: note: in expansion of macro ‘WARN_ONCE’ 46 | WARN_ONCE("Fix Pileup::calculateSimpleDNADouble numerical stability"); | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-SeqCoord.o `test -f 'SeqCoord.cpp' || echo './'`SeqCoord.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-MultiOverlap.o `test -f 'MultiOverlap.cpp' || echo './'`MultiOverlap.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-QualityVector.o `test -f 'QualityVector.cpp' || echo './'`QualityVector.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-SGAStats.o `test -f 'SGAStats.cpp' || echo './'`SGAStats.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-Quality.o `test -f 'Quality.cpp' || echo './'`Quality.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-PrimerScreen.o `test -f 'PrimerScreen.cpp' || echo './'`PrimerScreen.cpp In file included from /usr/include/c++/12/vector:70, from QualityVector.h:13, from QualityVector.cpp:13: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const DNADouble&}; _Tp = DNADouble; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = DNADouble; _Alloc = std::allocator]’, inlined from ‘void QualityVector::add(DNADouble)’ at QualityVector.cpp:33:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-BitVector.o `test -f 'BitVector.cpp' || echo './'`BitVector.cpp In file included from /usr/include/c++/12/vector:70, from Quality.h:13, from Quality.cpp:9: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘DoubleVector Quality::uniformLogProbVector(double, size_t)’ at Quality.cpp:18:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-CorrectionThresholds.o `test -f 'CorrectionThresholds.cpp' || echo './'`CorrectionThresholds.cpp In file included from /usr/include/c++/12/vector:70, from Util.h:12, from Match.h:13, from MultiOverlap.h:13, from MultiOverlap.cpp:13: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const MultiOverlap::MOData&}; _Tp = MultiOverlap::MOData; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-KmerDistribution.o `test -f 'KmerDistribution.cpp' || echo './'`KmerDistribution.cpp In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MultiOverlap::MOData; _Alloc = std::allocator]’, inlined from ‘void MultiOverlap::add(const std::string&, const Overlap&)’ at MultiOverlap.cpp:46:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MultiOverlap::MOData; _Alloc = std::allocator]’, inlined from ‘void MultiOverlap::add(const MOData&)’ at MultiOverlap.cpp:53:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-ClusterReader.o `test -f 'ClusterReader.cpp' || echo './'`ClusterReader.cpp /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AlphaCount&}; _Tp = AlphaCount; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {PUElem}; _Tp = PUElem; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {PUElem}; _Tp = PUElem; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-MultiAlignment.o `test -f 'MultiAlignment.cpp' || echo './'`MultiAlignment.cpp In file included from /usr/include/c++/12/algorithm:61, from MultiOverlap.cpp:10: /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/12/bits/stl_algo.h:60: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = MultiOverlap::MOData; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1900:25, inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27: /usr/include/c++/12/bits/stl_algo.h:1629:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1629 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const MultiOverlap::MOData&, const MultiOverlap::MOData&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘void MultiOverlap::print(int, int)’ at MultiOverlap.cpp:591:14: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const MultiOverlap::MOData&, const MultiOverlap::MOData&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘void MultiOverlap::print(int, int)’ at MultiOverlap.cpp:591:14: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-StdAlnTools.o `test -f 'StdAlnTools.cpp' || echo './'`StdAlnTools.cpp In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AlphaCount; _Alloc = std::allocator >]’, inlined from ‘std::string MultiOverlap::consensusConflict(double, int)’ at MultiOverlap.cpp:181:24: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-VCFUtil.o `test -f 'VCFUtil.cpp' || echo './'`VCFUtil.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-QualityTable.o `test -f 'QualityTable.cpp' || echo './'`QualityTable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-BloomFilter.o `test -f 'BloomFilter.cpp' || echo './'`BloomFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libutil_a-VariantIndex.o `test -f 'VariantIndex.cpp' || echo './'`VariantIndex.cpp In file included from /usr/include/c++/12/vector:63, from VCFUtil.h:14, from VCFUtil.cpp:14: /usr/include/c++/12/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = VCFRecord*]’: /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const VCFRecord&}; _Tp = VCFRecord; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = VCFRecord; _Alloc = std::allocator]’, inlined from ‘VCFReturnCode VCFUtil::generateVCFFromCancerVariant(const std::string&, const std::string&, const std::string&, const std::string&, size_t, const std::string&, int, double, int, VCFVector&)’ at VCFUtil.cpp:385:38: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = VCFRecord*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = VCFRecord*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = VCFRecord*; _Tp = VCFRecord]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = VCFRecord; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/vector.tcc:769:34, inlined from ‘void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = VCFRecord; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1779:19, inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = VCFRecord; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1481:22, inlined from ‘VCFReturnCode VCFUtil::generateVCFFromCancerVariant(const std::string&, const std::string&, const std::string&, const std::string&, size_t, const std::string&, int, double, int, VCFVector&)’ at VCFUtil.cpp:398:26: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = VCFRecord*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = VCFRecord*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = VCFRecord*; _Tp = VCFRecord]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = VCFRecord; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/vector.tcc:796:38, inlined from ‘void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = VCFRecord; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1779:19, inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = VCFRecord; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1481:22, inlined from ‘VCFReturnCode VCFUtil::generateVCFFromCancerVariant(const std::string&, const std::string&, const std::string&, const std::string&, size_t, const std::string&, int, double, int, VCFVector&)’ at VCFUtil.cpp:398:26: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -f libutil.a ar cru libutil.a libutil_a-Util.o libutil_a-Alphabet.o libutil_a-Contig.o libutil_a-ReadTable.o libutil_a-ReadInfoTable.o libutil_a-SeqReader.o libutil_a-DNAString.o libutil_a-Match.o libutil_a-Pileup.o libutil_a-BitChar.o libutil_a-Interval.o libutil_a-SeqCoord.o libutil_a-MultiOverlap.o libutil_a-QualityVector.o libutil_a-SGAStats.o libutil_a-Quality.o libutil_a-PrimerScreen.o libutil_a-BitVector.o libutil_a-CorrectionThresholds.o libutil_a-KmerDistribution.o libutil_a-ClusterReader.o libutil_a-MultiAlignment.o libutil_a-StdAlnTools.o libutil_a-VCFUtil.o libutil_a-QualityTable.o libutil_a-BloomFilter.o libutil_a-VariantIndex.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libutil.a make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Util' Making all in SQG make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/SQG' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -I../Util -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsqg_a-SQG.o `test -f 'SQG.cpp' || echo './'`SQG.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -I../Util -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsqg_a-ASQG.o `test -f 'ASQG.cpp' || echo './'`ASQG.cpp rm -f libsqg.a ar cru libsqg.a libsqg_a-SQG.o libsqg_a-ASQG.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libsqg.a make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/SQG' Making all in Bigraph make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Bigraph' g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libbigraph_a-Bigraph.o `test -f 'Bigraph.cpp' || echo './'`Bigraph.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libbigraph_a-Vertex.o `test -f 'Vertex.cpp' || echo './'`Vertex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libbigraph_a-Edge.o `test -f 'Edge.cpp' || echo './'`Edge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libbigraph_a-EdgeDesc.o `test -f 'EdgeDesc.cpp' || echo './'`EdgeDesc.cpp In file included from ../Util/EncodedString.h:22, from Vertex.h:23, from Vertex.cpp:9: ../Util/EncodedString.h: In instantiation of ‘void EncodedString::_copy(const EncodedString&) [with Codec = DNACodec]’: ../Util/EncodedString.h:43:18: required from ‘EncodedString::EncodedString(const EncodedString&) [with Codec = DNACodec]’ /usr/include/c++/12/bits/move.h:204:11: required from ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = EncodedString; _Require<__not_<__is_tuple_like<_Tp> >, is_move_constructible<_Tp>, is_move_assignable<_Tp> > = void]’ Vertex.cpp:46:18: required from here ../Util/EncodedString.h:236:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 236 | assert(m_capacity = other.m_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ rm -f libbigraph.a ar cru libbigraph.a libbigraph_a-Bigraph.o libbigraph_a-Vertex.o libbigraph_a-Edge.o libbigraph_a-EdgeDesc.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libbigraph.a make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Bigraph' Making all in Algorithm make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Algorithm' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-OverlapAlgorithm.o `test -f 'OverlapAlgorithm.cpp' || echo './'`OverlapAlgorithm.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-SearchSeed.o `test -f 'SearchSeed.cpp' || echo './'`SearchSeed.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-OverlapBlock.o `test -f 'OverlapBlock.cpp' || echo './'`OverlapBlock.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-SearchHistory.o `test -f 'SearchHistory.cpp' || echo './'`SearchHistory.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-ErrorCorrectProcess.o `test -f 'ErrorCorrectProcess.cpp' || echo './'`ErrorCorrectProcess.cpp In file included from SearchHistory.h:12, from OverlapBlock.h:15, from OverlapBlock.cpp:11: OverlapBlock.cpp: In member function ‘std::string OverlapBlock::getFullString(const std::string&) const’: ../Util/Util.h:32:53: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \ | ^~ OverlapBlock.cpp:88:9: note: in expansion of macro ‘WARN_ONCE’ 88 | WARN_ONCE("getFullString() called on block with no history") | ^~~~~~~~~ ../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 33 | printf("WARNING: [%s]\n", (x)); _warn_once = false; | ^~~~~~~~~~ OverlapBlock.cpp:88:9: note: in expansion of macro ‘WARN_ONCE’ 88 | WARN_ONCE("getFullString() called on block with no history") | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-QCProcess.o `test -f 'QCProcess.cpp' || echo './'`QCProcess.cpp In file included from /usr/include/c++/12/list:63, from ../SuffixTools/BWTInterval.h:13, from OverlapBlock.h:14: /usr/include/c++/12/bits/stl_list.h: In member function ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const OverlapBlock&}; _Tp = OverlapBlock; _Alloc = std::allocator]’: /usr/include/c++/12/bits/stl_list.h:2003:8: note: parameter passing for argument of type ‘std::__cxx11::list::iterator’ changed in GCC 7.1 2003 | _M_insert(iterator __position, _Args&&... __args) | ^~~~~~~~~ In file included from /usr/include/c++/12/map:60, from ../SuffixTools/STGlobals.h:15, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapBlock.h:17: /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/list:64, from ../Util/Util.h:13, from ../Util/Alphabet.h:29, from ../SuffixTools/STGlobals.h:19, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from OverlapAlgorithm.cpp:6: /usr/include/c++/12/bits/list.tcc: In member function ‘std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_iterator; = void; _Tp = OverlapBlock; _Alloc = std::allocator]’: /usr/include/c++/12/bits/list.tcc:133:7: note: parameter passing for argument of type ‘std::__cxx11::list::const_iterator’ changed in GCC 7.1 133 | list<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/list.tcc:133:7: note: parameter passing for argument of type ‘std::_List_iterator’ changed in GCC 7.1 /usr/include/c++/12/bits/list.tcc:133:7: note: parameter passing for argument of type ‘std::_List_iterator’ changed in GCC 7.1 In member function ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OverlapBlock; _Alloc = std::allocator]’, inlined from ‘OverlapBlockList resolveOverlap(const OverlapBlock&, const OverlapBlock&, const BWT*, const BWT*)’ at OverlapBlock.cpp:243:30: /usr/include/c++/12/bits/stl_list.h:1306:24: note: parameter passing for argument of type ‘std::_List_iterator’ changed in GCC 7.1 1306 | { this->_M_insert(end(), __x); } | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘OverlapBlockList resolveOverlap(const OverlapBlock&, const OverlapBlock&, const BWT*, const BWT*)’ at OverlapBlock.cpp:367:57: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘OverlapBlockList resolveOverlap(const OverlapBlock&, const OverlapBlock&, const BWT*, const BWT*)’ at OverlapBlock.cpp:370:36: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = long long int; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘OverlapBlockList resolveOverlap(const OverlapBlock&, const OverlapBlock&, const BWT*, const BWT*)’ at OverlapBlock.cpp:376:36: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ OverlapAlgorithm.cpp: In member function ‘OverlapResult OverlapAlgorithm::overlapReadExact(const SeqRecord&, int, OverlapBlockList*) const’: OverlapAlgorithm.cpp:150:24: note: parameter passing for argument of type ‘std::__cxx11::list::const_iterator’ changed in GCC 7.1 150 | oblSuffixFwd.insert(oblSuffixFwd.end(), oblFwdContain.begin(), oblFwdContain.end()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ OverlapAlgorithm.cpp:150:24: note: parameter passing for argument of type ‘std::_List_iterator’ changed in GCC 7.1 OverlapAlgorithm.cpp:151:24: note: parameter passing for argument of type ‘std::__cxx11::list::const_iterator’ changed in GCC 7.1 151 | oblPrefixFwd.insert(oblPrefixFwd.end(), oblFwdContain.begin(), oblFwdContain.end()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ OverlapAlgorithm.cpp:151:24: note: parameter passing for argument of type ‘std::_List_iterator’ changed in GCC 7.1 OverlapAlgorithm.cpp:152:24: note: parameter passing for argument of type ‘std::__cxx11::list::const_iterator’ changed in GCC 7.1 152 | oblSuffixRev.insert(oblSuffixRev.end(), oblRevContain.begin(), oblRevContain.end()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ OverlapAlgorithm.cpp:152:24: note: parameter passing for argument of type ‘std::_List_iterator’ changed in GCC 7.1 OverlapAlgorithm.cpp:153:24: note: parameter passing for argument of type ‘std::__cxx11::list::const_iterator’ changed in GCC 7.1 153 | oblPrefixRev.insert(oblPrefixRev.end(), oblRevContain.begin(), oblRevContain.end()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ OverlapAlgorithm.cpp:153:24: note: parameter passing for argument of type ‘std::_List_iterator’ changed in GCC 7.1 In file included from /usr/include/c++/12/algorithm:61, from ../SuffixTools/STGlobals.h:14: /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-OverlapTools.o `test -f 'OverlapTools.cpp' || echo './'`OverlapTools.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SearchSeed; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from ../SuffixTools/STGlobals.h:13: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const SearchSeed&}; _Tp = SearchSeed; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SearchSeed; _Alloc = std::allocator]’, inlined from ‘int OverlapAlgorithm::createSearchSeeds(const std::string&, const BWT*, const BWT*, int, int, SearchSeedVector*) const’ at OverlapAlgorithm.cpp:522:30, inlined from ‘bool OverlapAlgorithm::findOverlapBlocksInexact(const std::string&, const BWT*, const BWT*, const AlignFlags&, int, OverlapBlockList*, OverlapBlockList*, OverlapResult&) const’ at OverlapAlgorithm.cpp:324:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SearchSeed; _Alloc = std::allocator]’, inlined from ‘void OverlapAlgorithm::extendSeedsExactRight(const std::string&, const BWT*, const BWT*, ExtendDirection, const SearchSeedVector*, SearchSeedVector*) const’ at OverlapAlgorithm.cpp:584:34, inlined from ‘bool OverlapAlgorithm::findOverlapBlocksInexact(const std::string&, const BWT*, const BWT*, const AlignFlags&, int, OverlapBlockList*, OverlapBlockList*, OverlapResult&) const’ at OverlapAlgorithm.cpp:325:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SearchSeed; _Alloc = std::allocator]’, inlined from ‘void OverlapAlgorithm::extendSeedInexactRight(SearchSeed&, const std::string&, const BWT*, const BWT*, SearchSeedVector*) const’ at OverlapAlgorithm.cpp:597:30, inlined from ‘bool OverlapAlgorithm::findOverlapBlocksInexact(const std::string&, const BWT*, const BWT*, const AlignFlags&, int, OverlapBlockList*, OverlapBlockList*, OverlapResult&) const’ at OverlapAlgorithm.cpp:384:39: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SearchSeed; _Alloc = std::allocator]’, inlined from ‘void OverlapAlgorithm::extendSeedInexactRight(SearchSeed&, const std::string&, const BWT*, const BWT*, SearchSeedVector*) const’ at OverlapAlgorithm.cpp:608:34, inlined from ‘bool OverlapAlgorithm::findOverlapBlocksInexact(const std::string&, const BWT*, const BWT*, const AlignFlags&, int, OverlapBlockList*, OverlapBlockList*, OverlapResult&) const’ at OverlapAlgorithm.cpp:384:39: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SearchSeed; _Alloc = std::allocator]’, inlined from ‘void OverlapAlgorithm::extendSeedInexactRight(SearchSeed&, const std::string&, const BWT*, const BWT*, SearchSeedVector*) const’ at OverlapAlgorithm.cpp:630:38, inlined from ‘bool OverlapAlgorithm::findOverlapBlocksInexact(const std::string&, const BWT*, const BWT*, const AlignFlags&, int, OverlapBlockList*, OverlapBlockList*, OverlapResult&) const’ at OverlapAlgorithm.cpp:384:39: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SearchSeed; _Alloc = std::allocator]’, inlined from ‘void OverlapAlgorithm::extendSeedInexactLeft(SearchSeed&, const std::string&, const BWT*, const BWT*, SearchSeedVector*) const’ at OverlapAlgorithm.cpp:651:38, inlined from ‘bool OverlapAlgorithm::findOverlapBlocksInexact(const std::string&, const BWT*, const BWT*, const AlignFlags&, int, OverlapBlockList*, OverlapBlockList*, OverlapResult&) const’ at OverlapAlgorithm.cpp:386:38: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SearchSeed; _Alloc = std::allocator]’, inlined from ‘void OverlapAlgorithm::extendSeedInexactLeft(SearchSeed&, const std::string&, const BWT*, const BWT*, SearchSeedVector*) const’ at OverlapAlgorithm.cpp:677:42, inlined from ‘bool OverlapAlgorithm::findOverlapBlocksInexact(const std::string&, const BWT*, const BWT*, const AlignFlags&, int, OverlapBlockList*, OverlapBlockList*, OverlapResult&) const’ at OverlapAlgorithm.cpp:386:38: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const SearchSeed&, const SearchSeed&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘bool OverlapAlgorithm::findOverlapBlocksInexact(const std::string&, const BWT*, const BWT*, const AlignFlags&, int, OverlapBlockList*, OverlapBlockList*, OverlapResult&) const’ at OverlapAlgorithm.cpp:398:22: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const SearchSeed&, const SearchSeed&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘bool OverlapAlgorithm::findOverlapBlocksInexact(const std::string&, const BWT*, const BWT*, const AlignFlags&, int, OverlapBlockList*, OverlapBlockList*, OverlapResult&) const’ at OverlapAlgorithm.cpp:398:22: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-DPAlignment.o `test -f 'DPAlignment.cpp' || echo './'`DPAlignment.cpp In file included from /usr/include/c++/12/map:60, from ../SuffixTools/STGlobals.h:15, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from ErrorCorrectProcess.h:14, from ErrorCorrectProcess.cpp:10: /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-ConnectProcess.o `test -f 'ConnectProcess.cpp' || echo './'`ConnectProcess.cpp /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, ErrorCount>; _KeyOfValue = std::_Select1st, ErrorCount> >; _Compare = std::less >; _Alloc = std::allocator, ErrorCount> >]’: /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, ErrorCount>, std::_Select1st, ErrorCount> >, std::less >, std::allocator, ErrorCount> > >::const_iterator’ changed in GCC 7.1 g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-StringGraphGenerator.o `test -f 'StringGraphGenerator.cpp' || echo './'`StringGraphGenerator.cpp In file included from /usr/include/c++/12/map:61: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = ErrorCount; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void ErrorCountMap::incrementSample(const Key&) [with Key = long long int]’ at ../Util/Metrics.h:32:21, inlined from ‘void ErrorCorrectPostProcess::collectMetrics(const std::string&, const std::string&, const std::string&)’ at ErrorCorrectProcess.cpp:583:42: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = ErrorCount; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void ErrorCountMap::incrementSample(const Key&) [with Key = char]’ at ../Util/Metrics.h:32:21, inlined from ‘void ErrorCorrectPostProcess::collectMetrics(const std::string&, const std::string&, const std::string&)’ at ErrorCorrectProcess.cpp:586:45: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = ErrorCount; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void ErrorCountMap::incrementSample(const Key&) [with Key = char]’ at ../Util/Metrics.h:32:21, inlined from ‘void ErrorCorrectPostProcess::collectMetrics(const std::string&, const std::string&, const std::string&)’ at ErrorCorrectProcess.cpp:588:46: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = ErrorCount; _Compare = std::less >; _Alloc = std::allocator, ErrorCount> >]’, inlined from ‘void ErrorCountMap::incrementSample(const Key&) [with Key = std::__cxx11::basic_string]’ at ../Util/Metrics.h:32:21, inlined from ‘void ErrorCorrectPostProcess::collectMetrics(const std::string&, const std::string&, const std::string&)’ at ErrorCorrectProcess.cpp:594:50: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, ErrorCount>, std::_Select1st, ErrorCount> >, std::less >, std::allocator, ErrorCount> > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long int; _Tp = ErrorCount; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void ErrorCountMap::incrementError(const Key&) [with Key = long long int]’ at ../Util/Metrics.h:38:21, inlined from ‘void ErrorCorrectPostProcess::collectMetrics(const std::string&, const std::string&, const std::string&)’ at ErrorCorrectProcess.cpp:599:45: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = ErrorCount; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void ErrorCountMap::incrementError(const Key&) [with Key = char]’ at ../Util/Metrics.h:38:21, inlined from ‘void ErrorCorrectPostProcess::collectMetrics(const std::string&, const std::string&, const std::string&)’ at ErrorCorrectProcess.cpp:601:48: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = ErrorCount; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void ErrorCountMap::incrementError(const Key&) [with Key = char]’ at ../Util/Metrics.h:38:21, inlined from ‘void ErrorCorrectPostProcess::collectMetrics(const std::string&, const std::string&, const std::string&)’ at ErrorCorrectProcess.cpp:602:49: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = ErrorCount; _Compare = std::less >; _Alloc = std::allocator, ErrorCount> >]’, inlined from ‘void ErrorCountMap::incrementError(const Key&) [with Key = std::__cxx11::basic_string]’ at ../Util/Metrics.h:38:21, inlined from ‘void ErrorCorrectPostProcess::collectMetrics(const std::string&, const std::string&, const std::string&)’ at ErrorCorrectProcess.cpp:606:53: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, ErrorCount>, std::_Select1st, ErrorCount> >, std::less >, std::allocator, ErrorCount> > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-FMMergeProcess.o `test -f 'FMMergeProcess.cpp' || echo './'`FMMergeProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-StatsProcess.o `test -f 'StatsProcess.cpp' || echo './'`StatsProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-ClusterProcess.o `test -f 'ClusterProcess.cpp' || echo './'`ClusterProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-ReadCluster.o `test -f 'ReadCluster.cpp' || echo './'`ReadCluster.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-LRAlignment.o `test -f 'LRAlignment.cpp' || echo './'`LRAlignment.cpp In file included from /usr/include/c++/12/vector:70, from ../Util/Util.h:12, from FMMergeProcess.h:12, from FMMergeProcess.cpp:9: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BWTInterval&}; _Tp = BWTInterval; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/algorithm:61, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from FMMergeProcess.h:13: /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/12/bits/stl_algo.h:60: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = BWTInterval; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BWTInterval; _Alloc = std::allocator]’, inlined from ‘FMMergeResult FMMergeProcess::process(const SequenceWorkItem&)’ at FMMergeProcess.cpp:70:39: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BWTInterval; _Alloc = std::allocator]’, inlined from ‘FMMergeResult FMMergeProcess::process(const SequenceWorkItem&)’ at FMMergeProcess.cpp:107:47: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const BWTInterval&, const BWTInterval&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘FMMergeResult FMMergeProcess::process(const SequenceWorkItem&)’ at FMMergeProcess.cpp:148:18: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const BWTInterval&, const BWTInterval&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘FMMergeResult FMMergeProcess::process(const SequenceWorkItem&)’ at FMMergeProcess.cpp:148:18: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-StringThreader.o `test -f 'StringThreader.cpp' || echo './'`StringThreader.cpp LRAlignment.cpp: In function ‘void LRAlignment::removeDuplicateCells(LRStackEntry*, LRHash&)’: LRAlignment.cpp:560:34: warning: left shift count >= width of type [-Wshift-count-overflow] 560 | iter->second = i << 32 | p->G; | ~~^~~~~ LRAlignment.cpp:566:27: warning: left shift count >= width of type [-Wshift-count-overflow] 566 | hash[key] = i << 32 | p->G; | ~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-ExtensionDP.o `test -f 'ExtensionDP.cpp' || echo './'`ExtensionDP.cpp In file included from /usr/include/c++/12/vector:70, from ../Util/Util.h:12, from ReadCluster.h:13, from ReadCluster.cpp:10: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ClusterNode&}; _Tp = ClusterNode; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In constructor ‘ClusterNode::ClusterNode(ClusterNode&&)’, inlined from ‘ClusterNode ReadCluster::addSeed(const std::string&, bool)’ at ReadCluster.cpp:60:20: ReadCluster.h:17:8: warning: ‘emptyNode.ClusterNode::fwdCanonicalID’ may be used uninitialized [-Wmaybe-uninitialized] 17 | struct ClusterNode | ^~~~~~~~~~~ ReadCluster.cpp: In member function ‘ClusterNode ReadCluster::addSeed(const std::string&, bool)’: ReadCluster.cpp:55:25: note: ‘emptyNode.ClusterNode::fwdCanonicalID’ was declared here 55 | ClusterNode emptyNode; | ^~~~~~~~~ In constructor ‘ClusterNode::ClusterNode(ClusterNode&&)’, inlined from ‘ClusterNode ReadCluster::addSeed(const std::string&, bool)’ at ReadCluster.cpp:60:20: ReadCluster.h:17:8: warning: ‘emptyNode.ClusterNode::isReverseInterval’ may be used uninitialized [-Wmaybe-uninitialized] 17 | struct ClusterNode | ^~~~~~~~~~~ ReadCluster.cpp: In member function ‘ClusterNode ReadCluster::addSeed(const std::string&, bool)’: ReadCluster.cpp:55:25: note: ‘emptyNode.ClusterNode::isReverseInterval’ was declared here 55 | ClusterNode emptyNode; | ^~~~~~~~~ In file included from /usr/include/c++/12/algorithm:61, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from OverlapAlgorithm.h:13, from ReadCluster.h:14: /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/12/bits/stl_algo.h:60: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = ClusterNode; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const ClusterNode&, const ClusterNode&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘ClusterNodeVector ReadCluster::getOutput() const’ at ReadCluster.cpp:200:14: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const ClusterNode&, const ClusterNode&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘ClusterNodeVector ReadCluster::getOutput() const’ at ReadCluster.cpp:200:14: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from ../SuffixTools/STGlobals.h:13, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from LRAlignment.h:13, from LRAlignment.cpp:10: /usr/include/c++/12/bits/vector.tcc: In function ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = LRAlignment::LRHit; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 739 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-HaplotypeBuilder.o `test -f 'HaplotypeBuilder.cpp' || echo './'`HaplotypeBuilder.cpp /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const LRAlignment::LRCell&}; _Tp = LRAlignment::LRCell; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const LRAlignment::LRHit&}; _Tp = LRAlignment::LRHit; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ClusterNode; _Alloc = std::allocator]’, inlined from ‘void ReadCluster::run(size_t, int)’ at ReadCluster.cpp:117:35: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LRAlignment::LRHit; _Alloc = std::allocator]’, inlined from ‘void LRAlignment::saveTerminalHits(const SuffixArray*, const SampledSuffixArray*, const BWT*, LRStackEntry*, int, LRHitVector&)’ at LRAlignment.cpp:468:31: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LRAlignment::LRHit; _Alloc = std::allocator]’, inlined from ‘void LRAlignment::saveAllHits(const SuffixArray*, const SampledSuffixArray*, const BWT*, LRStackEntry*, int, LRHitVector&)’ at LRAlignment.cpp:430:27: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-GapFillProcess.o `test -f 'GapFillProcess.cpp' || echo './'`GapFillProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-VariationBuilderCommon.o `test -f 'VariationBuilderCommon.cpp' || echo './'`VariationBuilderCommon.cpp In file included from /usr/include/c++/12/algorithm:61, from ../SuffixTools/STGlobals.h:14: /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/12/bits/stl_algo.h:60: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = LRAlignment::LRHit; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const LRAlignment::LRHit&, const LRAlignment::LRHit&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int LRAlignment::resolveDuplicateHits(const BWT*, const SampledSuffixArray*, LRHitVector&, int)’ at LRAlignment.cpp:760:14: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const LRAlignment::LRHit&, const LRAlignment::LRHit&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int LRAlignment::resolveDuplicateHits(const BWT*, const SampledSuffixArray*, LRHitVector&, int)’ at LRAlignment.cpp:760:14: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LRAlignment::LRCell; _Alloc = std::allocator]’, inlined from ‘void LRAlignment::bwaswAlignment(const std::string&, const BWT*, const SampledSuffixArray*, const LRParams&, LRHitVector&)’ at LRAlignment.cpp:100:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LRAlignment::LRCell; _Alloc = std::allocator]’, inlined from ‘void LRAlignment::bwaswAlignment(const std::string&, const BWT*, const SampledSuffixArray*, const LRParams&, LRHitVector&)’ at LRAlignment.cpp:195:39: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LRAlignment::LRCell; _Alloc = std::allocator]’, inlined from ‘void LRAlignment::bwaswAlignment(const std::string&, const BWT*, const SampledSuffixArray*, const LRParams&, LRHitVector&)’ at LRAlignment.cpp:231:47: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = LRAlignment::LRHit; _Alloc = std::allocator]’, inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = LRAlignment::LRHit; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1481:22, inlined from ‘void LRAlignment::bwaswAlignment(const std::string&, const BWT*, const SampledSuffixArray*, const LRParams&, LRHitVector&)’ at LRAlignment.cpp:259:30: /usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 1779 | _M_range_insert(__pos, __first, __last, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 1780 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In member function ‘void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = LRAlignment::LRHit; _Alloc = std::allocator]’, inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = LRAlignment::LRHit; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1481:22, inlined from ‘void LRAlignment::bwaswAlignment(const std::string&, const BWT*, const SampledSuffixArray*, const LRParams&, LRHitVector&)’ at LRAlignment.cpp:264:19: /usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 1779 | _M_range_insert(__pos, __first, __last, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 1780 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LRAlignment::LRHit; _Alloc = std::allocator]’, inlined from ‘int LRAlignment::resolveDuplicateHitsByID(const BWT*, const SampledSuffixArray*, LRHitVector&, int)’ at LRAlignment.cpp:656:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const LRAlignment::LRHit&, const LRAlignment::LRHit&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int LRAlignment::resolveDuplicateHitsByID(const BWT*, const SampledSuffixArray*, LRHitVector&, int)’ at LRAlignment.cpp:664:14: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const LRAlignment::LRHit&, const LRAlignment::LRHit&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int LRAlignment::resolveDuplicateHitsByID(const BWT*, const SampledSuffixArray*, LRHitVector&, int)’ at LRAlignment.cpp:664:14: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const LRAlignment::LRHit&, const LRAlignment::LRHit&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int LRAlignment::resolveDuplicateHitsByID(const BWT*, const SampledSuffixArray*, LRHitVector&, int)’ at LRAlignment.cpp:679:14: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const LRAlignment::LRHit&, const LRAlignment::LRHit&)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from ‘int LRAlignment::resolveDuplicateHitsByID(const BWT*, const SampledSuffixArray*, LRHitVector&, int)’ at LRAlignment.cpp:679:14: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libalgorithm_a-KmerOverlaps.o `test -f 'KmerOverlaps.cpp' || echo './'`KmerOverlaps.cpp KmerOverlaps.cpp:60:12: warning: width of ‘KmerMatch::index’ exceeds its type 60 | size_t index:47; | ^~~~~ In file included from /usr/include/c++/12/vector:70, from ../Thirdparty/multiple_alignment.h:30, from KmerOverlaps.h:13, from KmerOverlaps.cpp:10: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ApproxSeed&}; _Tp = ApproxSeed; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ApproxSeed; _Alloc = std::allocator]’, inlined from ‘void _approximateSeededMatch(const std::string&, int, double, int, int, bool, const BWTIndexSet&, SequenceOverlapPairVector&)’ at KmerOverlaps.cpp:371:53: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ApproxSeed; _Alloc = std::allocator]’, inlined from ‘void _approximateSeededMatch(const std::string&, int, double, int, int, bool, const BWTIndexSet&, SequenceOverlapPairVector&)’ at KmerOverlaps.cpp:384:41: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ rm -f libalgorithm.a ar cru libalgorithm.a libalgorithm_a-OverlapAlgorithm.o libalgorithm_a-SearchSeed.o libalgorithm_a-OverlapBlock.o libalgorithm_a-SearchHistory.o libalgorithm_a-ErrorCorrectProcess.o libalgorithm_a-QCProcess.o libalgorithm_a-OverlapTools.o libalgorithm_a-DPAlignment.o libalgorithm_a-ConnectProcess.o libalgorithm_a-StringGraphGenerator.o libalgorithm_a-FMMergeProcess.o libalgorithm_a-StatsProcess.o libalgorithm_a-ClusterProcess.o libalgorithm_a-ReadCluster.o libalgorithm_a-LRAlignment.o libalgorithm_a-StringThreader.o libalgorithm_a-ExtensionDP.o libalgorithm_a-HaplotypeBuilder.o libalgorithm_a-GapFillProcess.o libalgorithm_a-VariationBuilderCommon.o libalgorithm_a-KmerOverlaps.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libalgorithm.a make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Algorithm' Making all in StringGraph make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/StringGraph' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-SGUtil.o `test -f 'SGUtil.cpp' || echo './'`SGUtil.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-SGAlgorithms.o `test -f 'SGAlgorithms.cpp' || echo './'`SGAlgorithms.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-SGVisitors.o `test -f 'SGVisitors.cpp' || echo './'`SGVisitors.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-CompleteOverlapSet.o `test -f 'CompleteOverlapSet.cpp' || echo './'`CompleteOverlapSet.cpp In file included from ../Bigraph/GraphCommon.h:14, from ../Bigraph/Bigraph.h:16, from SGAlgorithms.h:13, from SGAlgorithms.cpp:9: SGAlgorithms.cpp: In function ‘Edge* SGAlgorithms::createEdgesFromOverlap(StringGraph*, const Overlap&, bool, size_t)’: ../Util/Util.h:32:53: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \ | ^~ SGAlgorithms.cpp:60:9: note: in expansion of macro ‘WARN_ONCE’ 60 | WARN_ONCE("Edge limit reached for vertex when loading graph"); | ^~~~~~~~~ ../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 33 | printf("WARNING: [%s]\n", (x)); _warn_once = false; | ^~~~~~~~~~ SGAlgorithms.cpp:60:9: note: in expansion of macro ‘WARN_ONCE’ 60 | WARN_ONCE("Edge limit reached for vertex when loading graph"); | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-RemovalAlgorithm.o `test -f 'RemovalAlgorithm.cpp' || echo './'`RemovalAlgorithm.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-SGSearch.o `test -f 'SGSearch.cpp' || echo './'`SGSearch.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libstringgraph_a-SGWalk.o `test -f 'SGWalk.cpp' || echo './'`SGWalk.cpp rm -f libstringgraph.a ar cru libstringgraph.a libstringgraph_a-SGUtil.o libstringgraph_a-SGAlgorithms.o libstringgraph_a-SGVisitors.o libstringgraph_a-CompleteOverlapSet.o libstringgraph_a-RemovalAlgorithm.o libstringgraph_a-SGSearch.o libstringgraph_a-SGWalk.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libstringgraph.a make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/StringGraph' Making all in Concurrency make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Concurrency' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libconcurrency_a-OverlapProcess.o `test -f 'OverlapProcess.cpp' || echo './'`OverlapProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libconcurrency_a-RmdupProcess.o `test -f 'RmdupProcess.cpp' || echo './'`RmdupProcess.cpp rm -f libconcurrency.a ar cru libconcurrency.a libconcurrency_a-OverlapProcess.o libconcurrency_a-RmdupProcess.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libconcurrency.a make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Concurrency' Making all in SuffixTools make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/SuffixTools' g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-STCommon.o `test -f 'STCommon.cpp' || echo './'`STCommon.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-Occurrence.o `test -f 'Occurrence.cpp' || echo './'`Occurrence.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SuffixArray.o `test -f 'SuffixArray.cpp' || echo './'`SuffixArray.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SuffixCompare.o `test -f 'SuffixCompare.cpp' || echo './'`SuffixCompare.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-InverseSuffixArray.o `test -f 'InverseSuffixArray.cpp' || echo './'`InverseSuffixArray.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SACAInducedCopying.o `test -f 'SACAInducedCopying.cpp' || echo './'`SACAInducedCopying.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTAlgorithms.o `test -f 'BWTAlgorithms.cpp' || echo './'`BWTAlgorithms.cpp In file included from /usr/include/c++/12/vector:70, from STGlobals.h:13, from STCommon.h:11, from SuffixArray.h:11, from SuffixArray.cpp:9: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const SAElem&}; _Tp = SAElem; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SAElem; _Alloc = std::allocator]’, inlined from ‘void SuffixArray::removeReads(const NumericIDSet&)’ at SuffixArray.cpp:125:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTDiskConstruction.o `test -f 'BWTDiskConstruction.cpp' || echo './'`BWTDiskConstruction.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from STGlobals.h:14, from STCommon.h:11, from InverseSuffixArray.h:12, from InverseSuffixArray.cpp:10: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from STGlobals.h:13: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, inlined from ‘void InverseSuffixArray::validate() const’ at InverseSuffixArray.cpp:57:31: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from ‘void InverseSuffixArray::validate() const’ at InverseSuffixArray.cpp:61:14: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from ‘void InverseSuffixArray::validate() const’ at InverseSuffixArray.cpp:61:14: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTReader.o `test -f 'BWTReader.cpp' || echo './'`BWTReader.cpp In file included from ../Util/EncodedString.h:22, from Occurrence.h:13, from RLBWT.h:13, from BWT.h:18, from BWTDiskConstruction.h:19, from BWTDiskConstruction.cpp:12: ../Util/EncodedString.h: In instantiation of ‘void EncodedString::_copy(const EncodedString&) [with Codec = DNACodec]’: ../Util/EncodedString.h:43:18: required from ‘EncodedString::EncodedString(const EncodedString&) [with Codec = DNACodec]’ /usr/include/c++/12/bits/new_allocator.h:175:4: required from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString]’ /usr/include/c++/12/bits/alloc_traits.h:516:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString; allocator_type = std::allocator >]’ /usr/include/c++/12/bits/vector.tcc:117:30: required from ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {EncodedString}; _Tp = EncodedString; _Alloc = std::allocator >; reference = EncodedString&]’ /usr/include/c++/12/bits/stl_vector.h:1294:21: required from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = EncodedString; _Alloc = std::allocator >; value_type = EncodedString]’ BWTDiskConstruction.cpp:252:36: required from here ../Util/EncodedString.h:236:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 236 | assert(m_capacity = other.m_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTWriter.o `test -f 'BWTWriter.cpp' || echo './'`BWTWriter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SAReader.o `test -f 'SAReader.cpp' || echo './'`SAReader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SAWriter.o `test -f 'SAWriter.cpp' || echo './'`SAWriter.cpp In file included from /usr/include/c++/12/vector:70, from STGlobals.h:13, from STCommon.h:11, from SuffixArray.h:11, from BWTDiskConstruction.h:18: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const MergeItem&}; _Tp = MergeItem; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MergeItem; _Alloc = std::allocator]’, inlined from ‘MergeVector computeInitialSAIS(const BWTDiskParameters&)’ at BWTDiskConstruction.cpp:210:34: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-GapArray.o `test -f 'GapArray.cpp' || echo './'`GapArray.cpp In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MergeItem; _Alloc = std::allocator]’, inlined from ‘MergeVector computeInitialBCR(const BWTDiskParameters&)’ at BWTDiskConstruction.cpp:267:34: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from ../Util/Util.h:12, from SAReader.h:12, from SAReader.cpp:9: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const SAElem&}; _Tp = SAElem; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SAElem; _Alloc = std::allocator]’, inlined from ‘void SAReader::readElems(SAElemVector&)’ at SAReader.cpp:65:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-RankProcess.o `test -f 'RankProcess.cpp' || echo './'`RankProcess.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SBWT.o `test -f 'SBWT.cpp' || echo './'`SBWT.cpp In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MergeItem; _Alloc = std::allocator]’, inlined from ‘void buildBWTDisk(const BWTDiskParameters&)’ at BWTDiskConstruction.cpp:128:41: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MergeItem; _Alloc = std::allocator]’, inlined from ‘void buildBWTDisk(const BWTDiskParameters&)’ at BWTDiskConstruction.cpp:141:41: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from ../Util/Util.h:12, from RankProcess.h:13, from RankProcess.cpp:10: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]’, inlined from ‘RankResult RankProcess::process(const SequenceWorkItem&)’ at RankProcess.cpp:62:34: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]’, inlined from ‘RankResult RankProcess::process(const SequenceWorkItem&)’ at RankProcess.cpp:78:34: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]’, inlined from ‘RankResult RankProcess::process(const SequenceWorkItem&)’ at RankProcess.cpp:89:38: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-RLBWT.o `test -f 'RLBWT.cpp' || echo './'`RLBWT.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTWriterBinary.o `test -f 'BWTWriterBinary.cpp' || echo './'`BWTWriterBinary.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTReaderBinary.o `test -f 'BWTReaderBinary.cpp' || echo './'`BWTReaderBinary.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTWriterAscii.o `test -f 'BWTWriterAscii.cpp' || echo './'`BWTWriterAscii.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTReaderAscii.o `test -f 'BWTReaderAscii.cpp' || echo './'`BWTReaderAscii.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTIntervalCache.o `test -f 'BWTIntervalCache.cpp' || echo './'`BWTIntervalCache.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-QuickBWT.o `test -f 'QuickBWT.cpp' || echo './'`QuickBWT.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-SampledSuffixArray.o `test -f 'SampledSuffixArray.cpp' || echo './'`SampledSuffixArray.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTCABauerCoxRosone.o `test -f 'BWTCABauerCoxRosone.cpp' || echo './'`BWTCABauerCoxRosone.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-BWTCARopebwt.o `test -f 'BWTCARopebwt.cpp' || echo './'`BWTCARopebwt.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsuffixtools_a-PopulationIndex.o `test -f 'PopulationIndex.cpp' || echo './'`PopulationIndex.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from STGlobals.h:14, from STCommon.h:11, from SAWriter.h:13, from BWTCABauerCoxRosone.h:12, from BWTCABauerCoxRosone.cpp:9: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = BWTCA::BCRElem; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1844 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from ‘void BWTCA::runBauerCoxRosone(const DNAEncodedStringVector*, const std::string&, const std::string&)’ at BWTCABauerCoxRosone.cpp:59:18: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1940 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from ‘void BWTCA::runBauerCoxRosone(const DNAEncodedStringVector*, const std::string&, const std::string&)’ at BWTCABauerCoxRosone.cpp:79:14: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1940 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ rm -f libsuffixtools.a ar cru libsuffixtools.a libsuffixtools_a-STCommon.o libsuffixtools_a-Occurrence.o libsuffixtools_a-SuffixArray.o libsuffixtools_a-SuffixCompare.o libsuffixtools_a-InverseSuffixArray.o libsuffixtools_a-SACAInducedCopying.o libsuffixtools_a-BWTAlgorithms.o libsuffixtools_a-BWTDiskConstruction.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-SAReader.o libsuffixtools_a-SAWriter.o libsuffixtools_a-GapArray.o libsuffixtools_a-RankProcess.o libsuffixtools_a-SBWT.o libsuffixtools_a-RLBWT.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-BWTWriterBinary.o libsuffixtools_a-BWTReaderBinary.o libsuffixtools_a-BWTWriterAscii.o libsuffixtools_a-BWTReaderAscii.o libsuffixtools_a-BWTIntervalCache.o libsuffixtools_a-QuickBWT.o libsuffixtools_a-SampledSuffixArray.o libsuffixtools_a-BWTCABauerCoxRosone.o libsuffixtools_a-BWTCARopebwt.o libsuffixtools_a-PopulationIndex.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libsuffixtools.a make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/SuffixTools' Making all in Scaffold make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Scaffold' g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldVertex.o `test -f 'ScaffoldVertex.cpp' || echo './'`ScaffoldVertex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldEdge.o `test -f 'ScaffoldEdge.cpp' || echo './'`ScaffoldEdge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldGraph.o `test -f 'ScaffoldGraph.cpp' || echo './'`ScaffoldGraph.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldVisitors.o `test -f 'ScaffoldVisitors.cpp' || echo './'`ScaffoldVisitors.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldLink.o `test -f 'ScaffoldLink.cpp' || echo './'`ScaffoldLink.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldRecord.o `test -f 'ScaffoldRecord.cpp' || echo './'`ScaffoldRecord.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldGroup.o `test -f 'ScaffoldGroup.cpp' || echo './'`ScaffoldGroup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldSearch.o `test -f 'ScaffoldSearch.cpp' || echo './'`ScaffoldSearch.cpp In file included from /usr/include/c++/12/vector:70, from ../Bigraph/GraphCommon.h:13, from ScaffoldLink.h:14, from ScaffoldRecord.h:14, from ScaffoldRecord.cpp:11: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ScaffoldLink&}; _Tp = ScaffoldLink; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ScaffoldLink; _Alloc = std::allocator]’, inlined from ‘void ScaffoldRecord::addLink(const ScaffoldLink&)’ at ScaffoldRecord.cpp:32:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ScaffoldLink; _Alloc = std::allocator]’, inlined from ‘void ScaffoldRecord::parse(const std::string&)’ at ScaffoldRecord.cpp:340:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from ../Bigraph/GraphCommon.h:14, from ../Bigraph/Bigraph.h:16, from ScaffoldVertex.h:12, from ScaffoldGroup.h:13, from ScaffoldGroup.cpp:10: ScaffoldGroup.cpp: In member function ‘void ScaffoldGroup::getSecondaryLinks()’: ../Util/Util.h:32:53: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \ | ^~ ScaffoldGroup.cpp:279:13: note: in expansion of macro ‘WARN_ONCE’ 279 | WARN_ONCE("Recalculate xzDir"); | ^~~~~~~~~ ../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 33 | printf("WARNING: [%s]\n", (x)); _warn_once = false; | ^~~~~~~~~~ ScaffoldGroup.cpp:279:13: note: in expansion of macro ‘WARN_ONCE’ 279 | WARN_ONCE("Recalculate xzDir"); | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldWalk.o `test -f 'ScaffoldWalk.cpp' || echo './'`ScaffoldWalk.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldAlgorithms.o `test -f 'ScaffoldAlgorithms.cpp' || echo './'`ScaffoldAlgorithms.cpp In file included from /usr/include/c++/12/vector:70, from ../Bigraph/Bigraph.h:14: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const LinkVertexPair&}; _Tp = LinkVertexPair; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LinkVertexPair; _Alloc = std::allocator]’, inlined from ‘void ScaffoldGroup::addLink(const ScaffoldLink&, ScaffoldVertex*)’ at ScaffoldGroup.cpp:26:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LinkVertexPair; _Alloc = std::allocator]’, inlined from ‘void ScaffoldGroup::computeBestOrdering()’ at ScaffoldGroup.cpp:171:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ScaffoldLink&}; _Tp = ScaffoldLink; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ScaffoldLink; _Alloc = std::allocator]’, inlined from ‘void ScaffoldGroup::getLinearLinks(LinkVector&)’ at ScaffoldGroup.cpp:205:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ScaffoldLink; _Alloc = std::allocator]’, inlined from ‘void ScaffoldGroup::getLinearLinks(LinkVector&)’ at ScaffoldGroup.cpp:223:27: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libscaffold_a-ScaffoldSequenceCollection.o `test -f 'ScaffoldSequenceCollection.cpp' || echo './'`ScaffoldSequenceCollection.cpp rm -f libscaffold.a ar cru libscaffold.a libscaffold_a-ScaffoldVertex.o libscaffold_a-ScaffoldEdge.o libscaffold_a-ScaffoldGraph.o libscaffold_a-ScaffoldVisitors.o libscaffold_a-ScaffoldLink.o libscaffold_a-ScaffoldRecord.o libscaffold_a-ScaffoldGroup.o libscaffold_a-ScaffoldSearch.o libscaffold_a-ScaffoldWalk.o libscaffold_a-ScaffoldAlgorithms.o libscaffold_a-ScaffoldSequenceCollection.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libscaffold.a make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Scaffold' Making all in GraphDiff make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/GraphDiff' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-DindelUtil.o `test -f 'DindelUtil.cpp' || echo './'`DindelUtil.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-DindelRealignWindow.o `test -f 'DindelRealignWindow.cpp' || echo './'`DindelRealignWindow.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-DindelHMM.o `test -f 'DindelHMM.cpp' || echo './'`DindelHMM.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-OverlapHaplotypeBuilder.o `test -f 'OverlapHaplotypeBuilder.cpp' || echo './'`OverlapHaplotypeBuilder.cpp DindelRealignWindow.cpp: In member function ‘void DindelHaplotype::write(std::ostream&) const’: DindelRealignWindow.cpp:762:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 762 | for (size_t x=0; x::const_iterator i=it->second.begin();i!=it->second.end();i++) std::cout << " " << *i; std::cout << std::endl; | ^~~ DindelRealignWindow.cpp:1037:115: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 1037 | for (std::list::const_iterator i=it->second.begin();i!=it->second.end();i++) std::cout << " " << *i; std::cout << std::endl; | ^~~ DindelUtil.cpp: In function ‘DindelReturnCode DindelUtil::runDindelPairMatePair(const std::string&, const StringVector&, const StringVector&, const GraphCompareParameters&, std::ostream&, std::ostream&, std::ostream&, DindelReadReferenceAlignmentVector*)’: DindelUtil.cpp:65:10: warning: variable ‘has_complex_variant’ set but not used [-Wunused-but-set-variable] 65 | bool has_complex_variant = false; | ^~~~~~~~~~~~~~~~~~~ DindelRealignWindow.cpp: In member function ‘void DindelRealignWindow::computeHaplotypePairLikelihoods(std::vector&, std::unordered_map, std::__cxx11::list >&, const std::vector >&)’: DindelRealignWindow.cpp:2589:12: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2589 | for (int h1=0;h1&, const std::vector >&, double, int)’: DindelRealignWindow.cpp:2743:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2743 | for (size_t x=0;x&, const std::vector >&, double, int)’: DindelRealignWindow.cpp:2906:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2906 | for (size_t x=0;x::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = std::_Rb_tree_const_iterator; = void; _Tp = DindelReferenceMapping; _Alloc = std::allocator]’: /usr/include/c++/12/bits/stl_vector.h:702:9: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 702 | vector(_InputIterator __first, _InputIterator __last, | ^~~~~~ /usr/include/c++/12/bits/stl_vector.h:702:9: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {DindelRead}; _Tp = DindelRead; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {DindelRead}; _Tp = DindelRead; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DindelUtil.cpp: In function ‘DindelReturnCode DindelUtil::runDindelPairMatePair(const std::string&, const StringVector&, const StringVector&, const GraphCompareParameters&, std::ostream&, std::ostream&, std::ostream&, DindelReadReferenceAlignmentVector*)’: DindelUtil.cpp:247:91: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 247 | std::vector dRefMappings(refMappings.begin(),refMappings.end()); | ^ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-DeBruijnHaplotypeBuilder.o `test -f 'DeBruijnHaplotypeBuilder.cpp' || echo './'`DeBruijnHaplotypeBuilder.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o `test -f 'PairedDeBruijnHaplotypeBuilder.cpp' || echo './'`PairedDeBruijnHaplotypeBuilder.cpp DeBruijnHaplotypeBuilder.cpp: In member function ‘Vertex* DeBruijnHaplotypeBuilder::extendUnambiguously(Vertex*, StringGraph*, EdgeDir, size_t, size_t)’: DeBruijnHaplotypeBuilder.cpp:227:16: warning: variable ‘ext_count’ set but not used [-Wunused-but-set-variable] 227 | size_t ext_count = 0; | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-HapgenUtil.o `test -f 'HapgenUtil.cpp' || echo './'`HapgenUtil.cpp In file included from /usr/include/c++/12/vector:70, from ../Util/StdAlnTools.h:13, from DindelRealignWindow.cpp:28: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const DindelVariant&}; _Tp = DindelVariant; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-VCFTester.o `test -f 'VCFTester.cpp' || echo './'`VCFTester.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-GraphCompare.o `test -f 'GraphCompare.cpp' || echo './'`GraphCompare.cpp /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {DindelRealignWindowResult::HaplotypeProperties}; _Tp = DindelRealignWindowResult::HaplotypeProperties; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {DindelRealignWindowResult::HaplotypeProperties}; _Tp = DindelRealignWindowResult::HaplotypeProperties; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from ../SuffixTools/STGlobals.h:13, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from ../SuffixTools/BWTIndexSet.h:14, from HapgenUtil.h:14, from HapgenUtil.cpp:12: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BWTInterval&}; _Tp = BWTInterval; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const LocalAlignmentResult&}; _Tp = LocalAlignmentResult; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = LocalAlignmentResult; _Alloc = std::allocator]’, inlined from ‘LocalAlignmentResultVector HapgenUtil::alignReadsLocally(const std::string&, const SeqItemVector&)’ at HapgenUtil.cpp:603:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/map:60, from DindelRealignWindow.cpp:24: /usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = DindelVariant; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {LocalAlignmentResult}; _Tp = LocalAlignmentResult; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {LocalAlignmentResult}; _Tp = LocalAlignmentResult; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = LocalAlignmentResult; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘bool HapgenUtil::checkAlignmentsAreConsistent(const std::string&, const StringVector&)’ at HapgenUtil.cpp:437:29: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = DindelVariant; _Tp = DindelRealignWindowResult::GenotypeCall; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void DindelRealignWindow::addDiploidGenotypes(DindelRealignWindowResult&, const std::vector&, const std::vector >&)’ at DindelRealignWindow.cpp:2462:24: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = DindelVariant; _Tp = DindelRealignWindowResult::GenotypeCall; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void DindelRealignWindow::addDiploidGenotypes(DindelRealignWindowResult&, const std::vector&, const std::vector >&)’ at DindelRealignWindow.cpp:2485:53: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = DindelVariant; _Tp = DindelRealignWindowResult::GenotypeCall; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void DindelRealignWindow::addDiploidGenotypes(DindelRealignWindowResult&, const std::vector&, const std::vector >&)’ at DindelRealignWindow.cpp:2486:53: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = DindelVariant; _Tp = DindelRealignWindowResult::GenotypeCall; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void DindelRealignWindow::addDiploidGenotypes(DindelRealignWindowResult&, const std::vector&, const std::vector >&)’ at DindelRealignWindow.cpp:2504:69: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = DindelVariant; _Tp = DindelRealignWindowResult::GenotypeCall; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘void DindelRealignWindow::addDiploidGenotypes(DindelRealignWindowResult&, const std::vector&, const std::vector >&)’ at DindelRealignWindow.cpp:2505:69: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BWTInterval; _Alloc = std::allocator]’, inlined from ‘bool HapgenUtil::extractHaplotypeReads(const StringVector&, const BWTIndexSet&, int, bool, size_t, int64_t, SeqRecordVector*, SeqRecordVector*)’ at HapgenUtil.cpp:497:32: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-OverlapExtractorWithCorrection.o `test -f 'OverlapExtractorWithCorrection.cpp' || echo './'`OverlapExtractorWithCorrection.cpp In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘void DindelRealignWindow::setAddReadsSingleReadMultiSample(int, int, const std::vector >&, std::vector >&, std::vector&, int, int, std::vector&, std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::unordered_map, std::__cxx11::list >&)’ at DindelRealignWindow.cpp:3236:39: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = DindelVariant; _Alloc = std::allocator]’, inlined from ‘void DindelHaplotype::extractVariants()’ at DindelRealignWindow.cpp:648:41: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libgraphdiff_a-DBGPathGuide.o `test -f 'DBGPathGuide.cpp' || echo './'`DBGPathGuide.cpp In file included from /usr/include/c++/12/vector:63: /usr/include/c++/12/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelVariant*]’: /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelVariant*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelVariant*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelVariant*; _Tp = DindelVariant]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = DindelVariant; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = DindelVariant; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/vector.tcc:232:44: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelVariant*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelVariant*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelVariant*; _Tp = DindelVariant]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = DindelVariant; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from ‘std::vector WindowFile::getNextWindow()’ at DindelRealignWindow.cpp:4633:30: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = DindelVariant; _Alloc = std::allocator]’, inlined from ‘std::vector WindowFile::getNextWindow()’ at DindelRealignWindow.cpp:4654:31: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelReferenceMapping*]’: /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelReferenceMapping*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelReferenceMapping*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelReferenceMapping*; _Tp = DindelReferenceMapping]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = DindelReferenceMapping; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = DindelReferenceMapping; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/vector.tcc:232:44: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void DindelRealignWindow::computeProjectedMappingQuality()’ at DindelRealignWindow.cpp:1841:37: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void DindelRealignWindow::computeProjectedMappingQuality()’ at DindelRealignWindow.cpp:1852:44: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const VCFRecord&}; _Tp = VCFRecord; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void DindelRealignWindowResult::Inference::outputAsVCF(const DindelVariant&, const DindelRealignWindowResult&, VCFCollection&, const ReadTable*) const’ at DindelRealignWindow.cpp:1203:41: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void DindelRealignWindowResult::Inference::outputAsVCF(const DindelVariant&, const DindelRealignWindowResult&, VCFCollection&, const ReadTable*) const’ at DindelRealignWindow.cpp:1208:31: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = VCFRecord; _Alloc = std::allocator]’, inlined from ‘void DindelRealignWindowResult::Inference::outputAsVCF(const DindelVariant&, const DindelRealignWindowResult&, VCFCollection&, const ReadTable*) const’ at DindelRealignWindow.cpp:1409:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const DindelRead&}; _Tp = DindelRead; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = DindelRead; _Alloc = std::allocator]’, inlined from ‘void DindelRealignWindow::showHaplotypeOnlyReadsSingleRead(int, const std::vector >&, int, int)’ at DindelRealignWindow.cpp:3513:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = DindelRead; _Alloc = std::allocator]’, inlined from ‘void DindelRealignWindow::showHaplotypeOnlyReadsMatePairs(int, const std::vector >&, int, int)’ at DindelRealignWindow.cpp:3468:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = DindelRead; _Alloc = std::allocator]’, inlined from ‘void DindelRealignWindow::showHaplotypeOnlyReadsMatePairs(int, const std::vector >&, int, int)’ at DindelRealignWindow.cpp:3469:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {DindelHaplotype}; _Tp = DindelHaplotype; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {DindelHaplotype}; _Tp = DindelHaplotype; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = DindelHaplotype; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘DindelMultiHaplotype::DindelMultiHaplotype(const std::vector&, const std::string&, size_t)’ at DindelRealignWindow.cpp:937:31: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelHaplotype*]’: /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelHaplotype*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelHaplotype*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelHaplotype*; _Tp = DindelHaplotype]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = DindelHaplotype; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = DindelHaplotype; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from ‘DindelMultiHaplotype& DindelMultiHaplotype::operator=(const DindelMultiHaplotype&)’ at DindelRealignWindow.h:476:7: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelHaplotype*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelHaplotype*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelHaplotype*; _Tp = DindelHaplotype]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = DindelHaplotype; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from ‘DindelMultiHaplotype::DindelMultiHaplotype(const DindelMultiHaplotype&)’ at DindelRealignWindow.h:476:7: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelReferenceMapping*; bool _TrivialValueTypes = false]’, inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelReferenceMapping*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = DindelReferenceMapping*; _Tp = DindelReferenceMapping]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = DindelReferenceMapping; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from ‘DindelMultiHaplotype::DindelMultiHaplotype(const DindelMultiHaplotype&)’ at DindelRealignWindow.h:476:7: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -f libgraphdiff.a ar cru libgraphdiff.a libgraphdiff_a-DindelUtil.o libgraphdiff_a-DindelRealignWindow.o libgraphdiff_a-DindelHMM.o libgraphdiff_a-OverlapHaplotypeBuilder.o libgraphdiff_a-StringHaplotypeBuilder.o libgraphdiff_a-DeBruijnHaplotypeBuilder.o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o libgraphdiff_a-HapgenUtil.o libgraphdiff_a-VCFTester.o libgraphdiff_a-GraphCompare.o libgraphdiff_a-OverlapExtractorWithCorrection.o libgraphdiff_a-DBGPathGuide.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgraphdiff.a make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/GraphDiff' Making all in SGA make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/SGA' g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-sga.o `test -f 'sga.cpp' || echo './'`sga.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-index.o `test -f 'index.cpp' || echo './'`index.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-overlap.o `test -f 'overlap.cpp' || echo './'`overlap.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-assemble.o `test -f 'assemble.cpp' || echo './'`assemble.cpp index.cpp: In function ‘void parseIndexOptions(int, char**)’: index.cpp:276:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 276 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ overlap.cpp: In function ‘void parseOverlapOptions(int, char**)’: overlap.cpp:327:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 327 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from ../Util/EncodedString.h:22, from ../SuffixTools/Occurrence.h:13, from ../SuffixTools/RLBWT.h:13, from ../SuffixTools/BWT.h:18, from ../SuffixTools/BWTDiskConstruction.h:19, from index.cpp:18: ../Util/EncodedString.h: In instantiation of ‘void EncodedString::_copy(const EncodedString&) [with Codec = DNACodec]’: ../Util/EncodedString.h:43:18: required from ‘EncodedString::EncodedString(const EncodedString&) [with Codec = DNACodec]’ /usr/include/c++/12/bits/new_allocator.h:175:4: required from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString]’ /usr/include/c++/12/bits/alloc_traits.h:516:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = EncodedString; _Args = {EncodedString}; _Tp = EncodedString; allocator_type = std::allocator >]’ /usr/include/c++/12/bits/vector.tcc:117:30: required from ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {EncodedString}; _Tp = EncodedString; _Alloc = std::allocator >; reference = EncodedString&]’ /usr/include/c++/12/bits/stl_vector.h:1294:21: required from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = EncodedString; _Alloc = std::allocator >; value_type = EncodedString]’ index.cpp:130:27: required from here ../Util/EncodedString.h:236:31: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 236 | assert(m_capacity = other.m_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ assemble.cpp: In function ‘void parseAssembleOptions(int, char**)’: assemble.cpp:234:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 234 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-correct.o `test -f 'correct.cpp' || echo './'`correct.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-oview.o `test -f 'oview.cpp' || echo './'`oview.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-preprocess.o `test -f 'preprocess.cpp' || echo './'`preprocess.cpp correct.cpp: In function ‘void parseCorrectOptions(int, char**)’: correct.cpp:330:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 330 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ preprocess.cpp: In function ‘void parsePreprocessOptions(int, char**)’: preprocess.cpp:616:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 616 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-rmdup.o `test -f 'rmdup.cpp' || echo './'`rmdup.cpp oview.cpp: In function ‘void parseOviewOptions(int, char**)’: oview.cpp:202:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 202 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-merge.o `test -f 'merge.cpp' || echo './'`merge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-subgraph.o `test -f 'subgraph.cpp' || echo './'`subgraph.cpp rmdup.cpp: In function ‘void parseRmdupOptions(int, char**)’: rmdup.cpp:348:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 348 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ merge.cpp: In function ‘void parseMergeOptions(int, char**)’: merge.cpp:173:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 173 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-scaffold.o `test -f 'scaffold.cpp' || echo './'`scaffold.cpp subgraph.cpp: In function ‘void parseSubgraphOptions(int, char**)’: subgraph.cpp:169:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 169 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-scaffold2fasta.o `test -f 'scaffold2fasta.cpp' || echo './'`scaffold2fasta.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-connect.o `test -f 'connect.cpp' || echo './'`connect.cpp scaffold.cpp: In function ‘void parseScaffoldOptions(int, char**)’: scaffold.cpp:189:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 189 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ scaffold2fasta.cpp: In function ‘void parseScaffold2fastaOptions(int, char**)’: scaffold2fasta.cpp:196:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 196 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-walk.o `test -f 'walk.cpp' || echo './'`walk.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-filter.o `test -f 'filter.cpp' || echo './'`filter.cpp In file included from connect.cpp:15: connect.cpp: In function ‘int connectMain(int, char**)’: ../Util/Util.h:32:53: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 32 | #define WARN_ONCE(x) static bool _warn_once = true; if(_warn_once) \ | ^~ connect.cpp:297:17: note: in expansion of macro ‘WARN_ONCE’ 297 | WARN_ONCE("check orientation of result"); | ^~~~~~~~~ ../Util/Util.h:33:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 33 | printf("WARNING: [%s]\n", (x)); _warn_once = false; | ^~~~~~~~~~ connect.cpp:297:17: note: in expansion of macro ‘WARN_ONCE’ 297 | WARN_ONCE("check orientation of result"); | ^~~~~~~~~ connect.cpp: In function ‘void parseConnectOptions(int, char**)’: connect.cpp:465:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 465 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-kmer-count.o `test -f 'kmer-count.cpp' || echo './'`kmer-count.cpp walk.cpp: In function ‘void parseWalkOptions(int, char**)’: walk.cpp:323:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 323 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ filter.cpp: In function ‘void parseFilterOptions(int, char**)’: filter.cpp:217:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 217 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-stats.o `test -f 'stats.cpp' || echo './'`stats.cpp kmer-count.cpp: In function ‘void parseKmerCountOptions(int, char**)’: kmer-count.cpp:63:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 63 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-fm-merge.o `test -f 'fm-merge.cpp' || echo './'`fm-merge.cpp stats.cpp: In function ‘void parseStatsOptions(int, char**)’: stats.cpp:171:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 171 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-gmap.o `test -f 'gmap.cpp' || echo './'`gmap.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-filterBAM.o `test -f 'filterBAM.cpp' || echo './'`filterBAM.cpp fm-merge.cpp: In function ‘void parseFMMergeOptions(int, char**)’: fm-merge.cpp:164:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 164 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-cluster.o `test -f 'cluster.cpp' || echo './'`cluster.cpp gmap.cpp: In function ‘void parseGmapOptions(int, char**)’: gmap.cpp:303:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 303 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-gen-ssa.o `test -f 'gen-ssa.cpp' || echo './'`gen-ssa.cpp filterBAM.cpp: In function ‘void parseFilterBAMOptions(int, char**)’: filterBAM.cpp:438:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 438 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ cluster.cpp: In function ‘void parseClusterOptions(int, char**)’: cluster.cpp:292:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 292 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ gen-ssa.cpp: In function ‘void parseGenSSAOptions(int, char**)’: gen-ssa.cpp:108:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 108 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-bwt2fa.o `test -f 'bwt2fa.cpp' || echo './'`bwt2fa.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-graph-diff.o `test -f 'graph-diff.cpp' || echo './'`graph-diff.cpp bwt2fa.cpp: In function ‘void parseBWT2FAOptions(int, char**)’: bwt2fa.cpp:96:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 96 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-graph-concordance.o `test -f 'graph-concordance.cpp' || echo './'`graph-concordance.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp graph-diff.cpp: In function ‘void parseGraphDiffOptions(int, char**)’: graph-diff.cpp:493:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 493 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ graph-concordance.cpp: In function ‘std::string reconstructHaplotype(const VCFRecord&, VariantRecordVector, const ReadTable&, const BWTIndexSet&, size_t)’: graph-concordance.cpp:214:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 214 | if(end > chr.seq.length()) | ~~~~^~~~~~~~~~~~~~~~~~ graph-concordance.cpp: In function ‘void parseGraphConcordanceOptions(int, char**)’: graph-concordance.cpp:437:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 437 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ gapfill.cpp: In function ‘void parseGapFillOptions(int, char**)’: gapfill.cpp:148:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 148 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-preqc.o `test -f 'preqc.cpp' || echo './'`preqc.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-overlap-long.o `test -f 'overlap-long.cpp' || echo './'`overlap-long.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-variant-detectability.o `test -f 'variant-detectability.cpp' || echo './'`variant-detectability.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-rewrite-evidence-bam.o `test -f 'rewrite-evidence-bam.cpp' || echo './'`rewrite-evidence-bam.cpp overlap-long.cpp: In function ‘void parseOverlapLongOptions(int, char**)’: overlap-long.cpp:338:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 338 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from ../Thirdparty/rapidjson/reader.h:7, from ../Thirdparty/rapidjson/document.h:4, from preqc.cpp:27: ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF8::TakeBOM(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef170’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:170:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 170 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static rapidjson::UTF8::Ch rapidjson::UTF8::Take(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef183’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:183:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 183 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF8::PutBOM(OutputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef189’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:189:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 189 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF8::Put(OutputByteStream&, Ch)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef195’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:195:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 195 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF16::Encode(OutputStream&, unsigned int)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef219’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:219:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 219 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 2); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static bool rapidjson::UTF16::Decode(InputStream&, unsigned int*)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef234’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:234:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 234 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 2); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static bool rapidjson::UTF16::Validate(InputStream&, OutputStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef252’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:252:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 252 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 2); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef253’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:253:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 253 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 2); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF16LE::TakeBOM(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef271’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:271:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 271 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF16LE::Take(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef278’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:278:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 278 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF16LE::PutBOM(OutputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef286’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:286:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 286 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF16LE::Put(OutputByteStream&, CharType)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef292’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:292:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 292 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF16BE::TakeBOM(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef303’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:303:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 303 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF16BE::Take(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef310’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:310:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 310 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF16BE::PutBOM(OutputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef318’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:318:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 318 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF16BE::Put(OutputByteStream&, CharType)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef324’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:324:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 324 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF32::Encode(OutputStream&, unsigned int)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef348’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:348:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 348 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputStream::Ch) >= 4); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static bool rapidjson::UTF32::Decode(InputStream&, unsigned int*)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef355’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:355:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 355 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 4); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static bool rapidjson::UTF32::Validate(InputStream&, OutputStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef363’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:363:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 363 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputStream::Ch) >= 4); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF32LE::TakeBOM(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef375’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:375:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 375 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF32LE::Take(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef382’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:382:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 382 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF32LE::PutBOM(OutputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef392’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:392:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 392 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF32LE::Put(OutputByteStream&, CharType)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef398’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:398:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 398 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF32BE::TakeBOM(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef411’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:411:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 411 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static CharType rapidjson::UTF32BE::Take(InputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef418’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:418:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 418 | RAPIDJSON_STATIC_ASSERT(sizeof(typename InputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF32BE::PutBOM(OutputByteStream&)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef428’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:428:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 428 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h: In static member function ‘static void rapidjson::UTF32BE::Put(OutputByteStream&, CharType)’: ../Thirdparty/rapidjson/rapidjson.h:115:24: warning: typedef ‘StaticAssertTypedef434’ locally defined but not used [-Wunused-local-typedefs] 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:111:34: note: in definition of macro ‘RAPIDJSON_DO_JOIN2’ 111 | #define RAPIDJSON_DO_JOIN2(X, Y) X##Y | ^ ../Thirdparty/rapidjson/rapidjson.h:109:30: note: in expansion of macro ‘RAPIDJSON_DO_JOIN’ 109 | #define RAPIDJSON_JOIN(X, Y) RAPIDJSON_DO_JOIN(X, Y) | ^~~~~~~~~~~~~~~~~ ../Thirdparty/rapidjson/rapidjson.h:115:9: note: in expansion of macro ‘RAPIDJSON_JOIN’ 115 | RAPIDJSON_JOIN(StaticAssertTypedef, __LINE__) | ^~~~~~~~~~~~~~ ../Thirdparty/rapidjson/encodings.h:434:17: note: in expansion of macro ‘RAPIDJSON_STATIC_ASSERT’ 434 | RAPIDJSON_STATIC_ASSERT(sizeof(typename OutputByteStream::Ch) == 1); | ^~~~~~~~~~~~~~~~~~~~~~~ preqc.cpp: In function ‘void parsePreQCOptions(int, char**)’: preqc.cpp:2090:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 2090 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-somatic-variant-filters.o `test -f 'somatic-variant-filters.cpp' || echo './'`somatic-variant-filters.cpp variant-detectability.cpp: In function ‘void parseVarDetectOptions(int, char**)’: variant-detectability.cpp:205:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 205 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from rewrite-evidence-bam.cpp:18: /usr//include/bamtools/api/algorithms/Sort.h:64:18: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from rewrite-evidence-bam.cpp:10: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ rewrite-evidence-bam.cpp: In function ‘void parseRewriteEvidenceBAMOptions(int, char**)’: rewrite-evidence-bam.cpp:158:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 158 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-haplotype-filter.o `test -f 'haplotype-filter.cpp' || echo './'`haplotype-filter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sga-OverlapCommon.o `test -f 'OverlapCommon.cpp' || echo './'`OverlapCommon.cpp In file included from /usr/include/c++/12/queue:62, from preqc.cpp:14: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/12/algorithm:61, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/RLBWT.h:12, from ../SuffixTools/BWT.h:18, from preqc.h:14, from preqc.cpp:16: /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ somatic-variant-filters.cpp: In function ‘void parseSomaticVariantFiltersOptions(int, char**)’: somatic-variant-filters.cpp:794:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 794 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ haplotype-filter.cpp: In function ‘void parseHaplotypeFilterOptions(int, char**)’: haplotype-filter.cpp:1066:75: warning: comparison is always true due to limited range of data type [-Wtype-limits] 1066 | for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from ../SuffixTools/STGlobals.h:14, from ../SuffixTools/STCommon.h:11, from ../SuffixTools/BWTAlgorithms.h:12, from somatic-variant-filters.cpp:16: /usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/c++/12/queue:61: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void generate_gc_distribution(JSONWriter*, const BWTIndexSet&)’ at preqc.cpp:1108:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from ‘_Z25generate_duplication_ratePN9rapidjson12PrettyWriterINS_10FileStreamENS_4UTF8IcEES3_NS_19MemoryPoolAllocatorINS_12CrtAllocatorEEEEERK11BWTIndexSet._omp_fn.0’ at preqc.cpp:1230:18: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from ‘_Z25generate_duplication_ratePN9rapidjson12PrettyWriterINS_10FileStreamENS_4UTF8IcEES3_NS_19MemoryPoolAllocatorINS_12CrtAllocatorEEEEERK11BWTIndexSet._omp_fn.0’ at preqc.cpp:1230:18: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]’, inlined from ‘_Z25generate_duplication_ratePN9rapidjson12PrettyWriterINS_10FileStreamENS_4UTF8IcEES3_NS_19MemoryPoolAllocatorINS_12CrtAllocatorEEEEERK11BWTIndexSet._omp_fn.0’ at preqc.cpp:1227:35: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]’, inlined from ‘_Z25generate_duplication_ratePN9rapidjson12PrettyWriterINS_10FileStreamENS_4UTF8IcEES3_NS_19MemoryPoolAllocatorINS_12CrtAllocatorEEEEERK11BWTIndexSet._omp_fn.0’ at preqc.cpp:1217:35: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from ../Util/Util.h:12, from haplotype-filter.cpp:14: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector loadSampleDepthsFromFile(std::string)’ at haplotype-filter.cpp:973:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from ‘double median(std::vector) [with T = double]’ at somatic-variant-filters.cpp:131:14: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from ‘double median(std::vector) [with T = double]’ at somatic-variant-filters.cpp:131:14: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from ../Util/Util.h:12, from somatic-variant-filters.cpp:14: /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘CoverageStats getVariantCoverage(BamTools::BamReader*, const VCFRecord&, const ReadTable*)’ at somatic-variant-filters.cpp:290:34: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -Wextra -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/sga-qoWx2H/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fopenmp -L/usr//lib -L/usr//lib/bamtools -Wl,-z,relro -Wl,-z,now -o sga sga-sga.o sga-index.o sga-overlap.o sga-assemble.o sga-correct.o sga-oview.o sga-preprocess.o sga-rmdup.o sga-merge.o sga-subgraph.o sga-scaffold.o sga-scaffold2fasta.o sga-connect.o sga-walk.o sga-filter.o sga-kmer-count.o sga-stats.o sga-fm-merge.o sga-gmap.o sga-filterBAM.o sga-cluster.o sga-gen-ssa.o sga-bwt2fa.o sga-graph-diff.o sga-graph-concordance.o sga-gapfill.o sga-preqc.o sga-overlap-long.o sga-variant-detectability.o sga-rewrite-evidence-bam.o sga-somatic-variant-filters.o sga-haplotype-filter.o sga-OverlapCommon.o ../Scaffold/libscaffold.a ../GraphDiff/libgraphdiff.a ../StringGraph/libstringgraph.a ../Concurrency/libconcurrency.a ../Algorithm/libalgorithm.a ../SuffixTools/libsuffixtools.a ../Bigraph/libbigraph.a ../Util/libutil.a ../SQG/libsqg.a ../Thirdparty/libthirdparty.a -lz -lbamtools make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/SGA' make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src' make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src' make[2]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src' make[1]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src' dh_auto_test -a -O--sourcedirectory=src cd src && make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[1]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src' Making check in bin make[2]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/bin' Making check in Thirdparty make[2]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Thirdparty' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Thirdparty' Making check in Util make[2]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Util' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Util' Making check in SQG make[2]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/SQG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/SQG' Making check in Bigraph make[2]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Bigraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Bigraph' Making check in Algorithm make[2]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Algorithm' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Algorithm' Making check in StringGraph make[2]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/StringGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/StringGraph' Making check in Concurrency make[2]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Concurrency' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Concurrency' Making check in SuffixTools make[2]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/SuffixTools' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/SuffixTools' Making check in Scaffold make[2]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Scaffold' Making check in GraphDiff make[2]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/GraphDiff' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/GraphDiff' Making check in SGA make[2]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/SGA' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/SGA' make[2]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src' make[2]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src' make[1]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--sourcedirectory=src dh_prep -a -O--sourcedirectory=src debian/rules override_dh_auto_install make[1]: Entering directory '/build/sga-qoWx2H/sga-0.10.15' dh_auto_install cd src && make -j4 install DESTDIR=/build/sga-qoWx2H/sga-0.10.15/debian/sga AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src' Making install in bin make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/bin' make[4]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/bin' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/sga-qoWx2H/sga-0.10.15/debian/sga/usr/bin' /usr/bin/install -c sga-bam2de sga-mergeDriver '/build/sga-qoWx2H/sga-0.10.15/debian/sga/usr/bin' make[4]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/bin' make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/bin' Making install in Thirdparty make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Thirdparty' make[4]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Thirdparty' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Thirdparty' make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Thirdparty' Making install in Util make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Util' make[4]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Util' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Util' make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Util' Making install in SQG make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/SQG' make[4]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/SQG' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/SQG' make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/SQG' Making install in Bigraph make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Bigraph' make[4]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Bigraph' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Bigraph' make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Bigraph' Making install in Algorithm make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Algorithm' make[4]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Algorithm' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Algorithm' make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Algorithm' Making install in StringGraph make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/StringGraph' make[4]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/StringGraph' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/StringGraph' make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/StringGraph' Making install in Concurrency make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Concurrency' make[4]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Concurrency' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Concurrency' make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Concurrency' Making install in SuffixTools make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/SuffixTools' make[4]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/SuffixTools' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/SuffixTools' make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/SuffixTools' Making install in Scaffold make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Scaffold' make[4]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/Scaffold' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Scaffold' make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/Scaffold' Making install in GraphDiff make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/GraphDiff' make[4]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/GraphDiff' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/GraphDiff' make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/GraphDiff' Making install in SGA make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/SGA' make[4]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src/SGA' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/sga-qoWx2H/sga-0.10.15/debian/sga/usr/bin' /usr/bin/install -c sga '/build/sga-qoWx2H/sga-0.10.15/debian/sga/usr/bin' make[4]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/SGA' make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src/SGA' make[3]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src' make[4]: Entering directory '/build/sga-qoWx2H/sga-0.10.15/src' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src' make[3]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src' make[2]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15/src' cp -a src/bin/sga-bam2de.pl debian/sga/usr/bin/sga-bam2de cp -a src/bin/sga-astat.py debian/sga/usr/bin/sga-astat make[1]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15' dh_install -a -O--sourcedirectory=src dh_installdocs -a -O--sourcedirectory=src dh_installchangelogs -a -O--sourcedirectory=src debian/rules override_dh_installexamples make[1]: Entering directory '/build/sga-qoWx2H/sga-0.10.15' dh_installexamples mkdir -p debian/sga/usr/share/doc/sga/examples sed -e 's?^\(SGA_BIN=sga\).*?\1?' \ -e 's?^.*/bin/sga-align?sga-align?' \ -e 's?^.*/bin/sga-bam2de.pl?sga-bam2de?' \ -e 's?^.*/bin/sga-astat.py?sga-astat?' \ src/examples/sga-celegans.sh > debian/sga/usr/share/doc/sga/examples/sga-celegans.sh make[1]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15' debian/rules override_dh_installman make[1]: Entering directory '/build/sga-qoWx2H/sga-0.10.15' dh_installman mkdir -p /build/sga-qoWx2H/sga-0.10.15/debian/sga/usr/share/man/man1/ PATH=/usr/lib/abyss:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games \ help2man \ --version-string="0.10.15" \ --no-info \ --name "Make a distance estimate file from a bam file of reads aligned to contigs" \ --output /build/sga-qoWx2H/sga-0.10.15/debian/sga/usr/share/man/man1//sga-bam2de.1 \ /build/sga-qoWx2H/sga-0.10.15/debian/sga/usr/bin/sga-bam2de help2man \ --no-info \ --version-string="0.10.15" \ --name="String Graph Assembler: de novo genome assembler that uses string graphs" \ --output /build/sga-qoWx2H/sga-0.10.15/debian/sga/usr/share/man/man1//sga.1 \ /build/sga-qoWx2H/sga-0.10.15/debian/sga/usr/bin/sga help2man \ --no-info\ --version-string="0.10.15" \ --name="generate sga merge commands from a list of files" \ --output /build/sga-qoWx2H/sga-0.10.15/debian/sga/usr/share/man/man1//sga-mergeDriver.1 \ /build/sga-qoWx2H/sga-0.10.15/debian/sga/usr/bin/sga-mergeDriver make[1]: Leaving directory '/build/sga-qoWx2H/sga-0.10.15' dh_python3 -a -O--sourcedirectory=src dh_installsystemduser -a -O--sourcedirectory=src dh_perl -a -O--sourcedirectory=src dh_link -a -O--sourcedirectory=src dh_strip_nondeterminism -a -O--sourcedirectory=src dh_compress -a -O--sourcedirectory=src dh_fixperms -a -O--sourcedirectory=src dh_missing -a -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dpkg-shlibdeps: warning: debian/sga/usr/bin/sga contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a -O--sourcedirectory=src dh_gencontrol -a -O--sourcedirectory=src dh_md5sums -a -O--sourcedirectory=src dh_builddeb -a -O--sourcedirectory=src dpkg-deb: building package 'sga' in '../sga_0.10.15-7+b1_armel.deb'. dpkg-deb: building package 'sga-dbgsym' in '../sga-dbgsym_0.10.15-7+b1_armel.deb'. dpkg-genbuildinfo --build=any -O../sga_0.10.15-7+b1_armel.buildinfo dpkg-genchanges --build=any -O../sga_0.10.15-7+b1_armel.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 2025-07-28T23:01:09Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 28 Jul 2025 23:01:10 +0000 | +------------------------------------------------------------------------------+ sga_0.10.15-7+b1_armel.changes: ------------------------------- Format: 1.8 Date: Fri, 02 Sep 2022 20:56:15 +0000 Source: sga (0.10.15-7) Binary: sga sga-dbgsym Binary-Only: yes Architecture: armel Version: 0.10.15-7+b1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team Changed-By: armel Build Daemon (henze) Description: sga - de novo genome assembler that uses string graphs Changes: sga (0.10.15-7+b1) sid; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for armel; no source changes. * Rebuild against libbamtools2.5.2 Checksums-Sha1: e7a8250d122e87280e02299a7c5b8baa4c1f5cae 12892952 sga-dbgsym_0.10.15-7+b1_armel.deb f233799621dc6f626d1dcdffb795cae42493c601 8217 sga_0.10.15-7+b1_armel.buildinfo ff5abaca681abbeedf25aae3030c30fd5d6d1b90 577792 sga_0.10.15-7+b1_armel.deb Checksums-Sha256: 3ea60b3c245b39f9d4b055ed65ff4bc239b7f0a947c4ab3b2c361319dcf6b408 12892952 sga-dbgsym_0.10.15-7+b1_armel.deb 1e553dca2ef86700f950fe14977bb0fbf1b0ea0aeff2bfdd58a0b3eaf5648dcd 8217 sga_0.10.15-7+b1_armel.buildinfo 12a935a4458cb2a14286f4456409ed5b4daa526fb508ff5f8350f30eb6b84779 577792 sga_0.10.15-7+b1_armel.deb Files: 1939cd778ad71289a7f18477e7e69efd 12892952 debug optional sga-dbgsym_0.10.15-7+b1_armel.deb 19224f24c5ef2b1c51ee374e43b17dd4 8217 science optional sga_0.10.15-7+b1_armel.buildinfo 0ee5e44d0f6ae839d9ba87fe235485ef 577792 science optional sga_0.10.15-7+b1_armel.deb +------------------------------------------------------------------------------+ | Buildinfo Mon, 28 Jul 2025 23:01:11 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: sga (0.10.15-7) Binary: sga sga-dbgsym Architecture: armel Version: 0.10.15-7+b1 Binary-Only-Changes: sga (0.10.15-7+b1) sid; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for armel; no source changes. * Rebuild against libbamtools2.5.2 . -- armel Build Daemon (henze) Fri, 02 Sep 2022 20:56:15 +0000 Checksums-Md5: 1939cd778ad71289a7f18477e7e69efd 12892952 sga-dbgsym_0.10.15-7+b1_armel.deb 0ee5e44d0f6ae839d9ba87fe235485ef 577792 sga_0.10.15-7+b1_armel.deb Checksums-Sha1: e7a8250d122e87280e02299a7c5b8baa4c1f5cae 12892952 sga-dbgsym_0.10.15-7+b1_armel.deb ff5abaca681abbeedf25aae3030c30fd5d6d1b90 577792 sga_0.10.15-7+b1_armel.deb Checksums-Sha256: 3ea60b3c245b39f9d4b055ed65ff4bc239b7f0a947c4ab3b2c361319dcf6b408 12892952 sga-dbgsym_0.10.15-7+b1_armel.deb 12a935a4458cb2a14286f4456409ed5b4daa526fb508ff5f8350f30eb6b84779 577792 sga_0.10.15-7+b1_armel.deb Build-Origin: Debian Build-Architecture: armel Build-Date: Mon, 28 Jul 2025 23:01:09 +0000 Build-Path: /build/sga-qoWx2H/sga-0.10.15 Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-9), autotools-dev (= 20220109.1), base-files (= 12.2), base-passwd (= 3.6.0), bash (= 5.2~rc2-2), binutils (= 2.38.90.20220713-2), binutils-arm-linux-gnueabi (= 2.38.90.20220713-2), binutils-common (= 2.38.90.20220713-2), bsdextrautils (= 2.38.1-1), bsdutils (= 1:2.38.1-1), build-essential (= 12.9), bzip2 (= 1.0.8-5), coreutils (= 8.32-4.1), cpp (= 4:12.2.0-1), cpp-12 (= 12.2.0-1), dash (= 0.5.11+git20210903+057cd650a4ed-8), debconf (= 1.5.79), debhelper (= 13.9.1), debianutils (= 5.7-0.3), dh-autoreconf (= 20), dh-python (= 5.20220819), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-1), dmsetup (= 2:1.02.185-1), dpkg (= 1.21.9), dpkg-dev (= 1.21.9), dwz (= 0.14-1), file (= 1:5.41-4), findutils (= 4.9.0-3), fontconfig (= 2.13.1-4.4), fontconfig-config (= 2.13.1-4.4), fonts-dejavu-core (= 2.37-2), g++ (= 4:12.2.0-1), g++-12 (= 12.2.0-1), gcc (= 4:12.2.0-1), gcc-12 (= 12.2.0-1), gcc-12-base (= 12.2.0-1), gettext (= 0.21-9), gettext-base (= 0.21-9), graphviz (= 2.42.2-7), grep (= 3.7-1), groff-base (= 1.22.4-8), gzip (= 1.12-1), help2man (= 1.49.2), hostname (= 3.23), init-system-helpers (= 1.64), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libapparmor1 (= 3.0.7-1), libarchive-zip-perl (= 1.68-1), libargon2-1 (= 0~20171227-0.3), libasan8 (= 12.2.0-1), libatomic1 (= 12.2.0-1), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0.7-1), libaudit1 (= 1:3.0.7-1+b1), libbamtools-dev (= 2.5.2+dfsg-2), libbamtools2.5.2 (= 2.5.2+dfsg-2), libbinutils (= 2.38.90.20220713-2), libblkid1 (= 2.38.1-1), libbrotli1 (= 1.0.9-2+b4), libbsd0 (= 0.11.6-1), libbz2-1.0 (= 1.0.8-5), libc-bin (= 2.34-7), libc-dev-bin (= 2.34-7), libc6 (= 2.34-7), libc6-dev (= 2.34-7), libcairo2 (= 1.16.0-6), libcap-ng0 (= 0.8.3-1+b1), libcap2 (= 1:2.44-1), libcc1-0 (= 12.2.0-1), libcdt5 (= 2.42.2-7), libcgraph6 (= 2.42.2-7), libcom-err2 (= 1.46.5-2), libcrypt-dev (= 1:4.4.28-2), libcrypt1 (= 1:4.4.28-2), libcryptsetup12 (= 2:2.5.0-2), libctf-nobfd0 (= 2.38.90.20220713-2), libctf0 (= 2.38.90.20220713-2), libcurl3-gnutls (= 7.85.0-1), libdatrie1 (= 0.2.13-2), libdb5.3 (= 5.3.28+dfsg1-0.10), libdebconfclient0 (= 0.264), libdebhelper-perl (= 13.9.1), libdeflate0 (= 1.12-1), libdevmapper1.02.1 (= 2:1.02.185-1), libdpkg-perl (= 1.21.9), libelf1 (= 0.187-1), libexpat1 (= 2.4.8-1), libfdisk1 (= 2.38.1-1), libffi8 (= 3.4.2-4), libfile-stripnondeterminism-perl (= 1.13.0-1), libfontconfig1 (= 2.13.1-4.4), libfreetype6 (= 2.12.1+dfsg-3), libfribidi0 (= 1.0.8-2.1), libgcc-12-dev (= 12.2.0-1), libgcc-s1 (= 12.2.0-1), libgcrypt20 (= 1.10.1-2), libgd3 (= 2.3.3-6), libgdbm-compat4 (= 1.23-1+b1), libgdbm6 (= 1.23-1+b1), libglib2.0-0 (= 2.73.3-3), libgmp10 (= 2:6.2.1+dfsg1-1), libgnutls30 (= 3.7.7-2), libgomp1 (= 12.2.0-1), libgpg-error0 (= 1.45-2), libgraphite2-3 (= 1.3.14-1), libgssapi-krb5-2 (= 1.20-1), libgts-0.7-5 (= 0.7.6+darcs121130-5), libgvc6 (= 2.42.2-7), libgvpr2 (= 2.42.2-7), libharfbuzz0b (= 2.7.4-1+b1), libhogweed6 (= 3.8.1-2), libhts3 (= 1.13+ds-2+b1), libhtscodecs2 (= 1.2.2-1), libice6 (= 2:1.0.10-1), libicu71 (= 71.1-3), libidn2-0 (= 2.3.3-1+b1), libip4tc2 (= 1.8.8-1), libisl23 (= 0.25-1), libjbig0 (= 2.1-3.1+b2), libjpeg62-turbo (= 1:2.1.2-1), libjson-c5 (= 0.16-1), libk5crypto3 (= 1.20-1), libkeyutils1 (= 1.6.3-1), libkmod2 (= 30+20220630-3), libkrb5-3 (= 1.20-1), libkrb5support0 (= 1.20-1), liblab-gamut1 (= 2.42.2-7), libldap-2.5-0 (= 2.5.12+dfsg-2+b1), liblerc4 (= 4.0.0+ds-1), liblocale-gettext-perl (= 1.07-4+b2), libltdl7 (= 2.4.7-4), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.2.5-2.1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmd0 (= 1.0.4-2), libmount1 (= 2.38.1-1), libmpc3 (= 1.2.1-2), libmpdec3 (= 2.5.1-2), libmpfr6 (= 4.1.0-3), libncurses6 (= 6.3+20220423-2), libncursesw6 (= 6.3+20220423-2), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.49.0-1), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libp11-kit0 (= 0.24.1-1), libpam-modules (= 1.5.2-2), libpam-modules-bin (= 1.5.2-2), libpam-runtime (= 1.5.2-2), libpam0g (= 1.5.2-2), libpango-1.0-0 (= 1.50.9+ds-1), libpangocairo-1.0-0 (= 1.50.9+ds-1), libpangoft2-1.0-0 (= 1.50.9+ds-1), libpathplan4 (= 2.42.2-7), libpcre2-8-0 (= 10.40-1), libpcre3 (= 2:8.39-14), libperl5.34 (= 5.34.0-5), libpipeline1 (= 1.5.6-2), libpixman-1-0 (= 0.40.0-1), libpng16-16 (= 1.6.37-5), libpsl5 (= 0.21.0-1.2), libpython3-stdlib (= 3.10.6-1), libpython3.10-minimal (= 3.10.6-1), libpython3.10-stdlib (= 3.10.6-1), libreadline8 (= 8.2~rc2-2), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2), libsasl2-2 (= 2.1.28+dfsg-7), libsasl2-modules-db (= 2.1.28+dfsg-7), libseccomp2 (= 2.5.4-1+b1), libselinux1 (= 3.4-1+b1), libsm6 (= 2:1.2.3-1), libsmartcols1 (= 2.38.1-1), libsparsehash-dev (= 2.0.3-2), libsqlite3-0 (= 3.39.2-1), libssh2-1 (= 1.10.0-3+b1), libssl3 (= 3.0.5-2), libstdc++-12-dev (= 12.2.0-1), libstdc++6 (= 12.2.0-1), libsub-override-perl (= 0.09-3), libsystemd-shared (= 251.4-3), libsystemd0 (= 251.4-3), libtasn1-6 (= 4.18.0-4), libthai-data (= 0.1.29-1), libthai0 (= 0.1.29-1), libtiff5 (= 4.4.0-4), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-4), libubsan1 (= 12.2.0-1), libuchardet0 (= 0.0.7-1), libudev1 (= 251.4-3), libunistring2 (= 1.0-1), libuuid1 (= 2.38.1-1), libwebp7 (= 1.2.2-2+b1), libx11-6 (= 2:1.8.1-2), libx11-data (= 2:1.8.1-2), libxau6 (= 1:1.0.9-1), libxaw7 (= 2:1.0.14-1), libxcb-render0 (= 1.15-1), libxcb-shm0 (= 1.15-1), libxcb1 (= 1.15-1), libxdmcp6 (= 1:1.1.2-3), libxext6 (= 2:1.3.4-1), libxml2 (= 2.9.14+dfsg-1+b1), libxmu6 (= 2:1.1.3-3), libxpm4 (= 1:3.5.12-1), libxrender1 (= 1:0.9.10-1.1), libxt6 (= 1:1.2.1-1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.18.16-1), login (= 1:4.11.1+dfsg1-2), lsb-base (= 11.2), m4 (= 1.4.19-1), make (= 4.3-4.1), man-db (= 2.10.2-2), mawk (= 1.3.4.20200120-3.1), media-types (= 8.0.0), mount (= 2.38.1-1), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), patch (= 2.7.6-7), perl (= 5.34.0-5), perl-base (= 5.34.0-5), perl-modules-5.34 (= 5.34.0-5), po-debconf (= 1.0.21+nmu1), python3 (= 3.10.6-1), python3-distutils (= 3.10.6-1), python3-lib2to3 (= 3.10.6-1), python3-minimal (= 3.10.6-1), python3-pysam (= 0.17.0+ds-2+b2), python3-ruffus (= 2.8.4-4), python3.10 (= 3.10.6-1), python3.10-minimal (= 3.10.6-1), readline-common (= 8.2~rc2-2), rpcsvc-proto (= 1.4.2-4), samtools (= 1.13-4), sed (= 4.8-1), sensible-utils (= 0.0.17), systemd (= 251.4-3), sysvinit-utils (= 3.04-1), tar (= 1.34+dfsg-1), ucf (= 3.0043), util-linux (= 2.38.1-1), util-linux-extra (= 2.38.1-1), x11-common (= 1:7.7+23), xz-utils (= 5.2.5-2.1), zlib1g (= 1:1.2.11.dfsg-4.1), zlib1g-dev (= 1:1.2.11.dfsg-4.1) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1662152175" +------------------------------------------------------------------------------+ | Package contents Mon, 28 Jul 2025 23:01:11 +0000 | +------------------------------------------------------------------------------+ sga-dbgsym_0.10.15-7+b1_armel.deb --------------------------------- new Debian package, version 2.0. size 12892952 bytes: control archive=540 bytes. 378 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: sga-dbgsym Source: sga (0.10.15-7) Version: 0.10.15-7+b1 Auto-Built-Package: debug-symbols Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 12890 Depends: sga (= 0.10.15-7+b1) Section: debug Priority: optional Description: debug symbols for sga Build-Ids: ada06bc0269f186b981d7835f4851b008304d29f drwxr-xr-x root/root 0 2022-09-02 20:56 ./ drwxr-xr-x root/root 0 2022-09-02 20:56 ./usr/ drwxr-xr-x root/root 0 2022-09-02 20:56 ./usr/lib/ drwxr-xr-x root/root 0 2022-09-02 20:56 ./usr/lib/debug/ drwxr-xr-x root/root 0 2022-09-02 20:56 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2022-09-02 20:56 ./usr/lib/debug/.build-id/ad/ -rw-r--r-- root/root 13188660 2022-09-02 20:56 ./usr/lib/debug/.build-id/ad/a06bc0269f186b981d7835f4851b008304d29f.debug drwxr-xr-x root/root 0 2022-09-02 20:56 ./usr/share/ drwxr-xr-x root/root 0 2022-09-02 20:56 ./usr/share/doc/ lrwxrwxrwx root/root 0 2022-09-02 20:56 ./usr/share/doc/sga-dbgsym -> sga sga_0.10.15-7+b1_armel.deb -------------------------- new Debian package, version 2.0. size 577792 bytes: control archive=1312 bytes. 895 bytes, 18 lines control 1144 bytes, 18 lines md5sums Package: sga Source: sga (0.10.15-7) Version: 0.10.15-7+b1 Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 1727 Depends: libbamtools2.5.2 (>= 2.5.2+dfsg), libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libstdc++6 (>= 11), zlib1g (>= 1:1.1.4), python3:any, perl:any, samtools, python3-ruffus, python3-pysam Recommends: abyss Section: science Priority: optional Homepage: https://github.com/jts/sga Description: de novo genome assembler that uses string graphs The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads. . SGA is a de novo assembler for DNA sequence reads. It is based on Gene Myers' string graph formulation of assembly and uses the FM-index/Burrows-Wheeler transform to efficiently find overlaps between sequence reads. drwxr-xr-x root/root 0 2022-09-02 20:56 ./ drwxr-xr-x root/root 0 2022-09-02 20:56 ./usr/ drwxr-xr-x root/root 0 2022-09-02 20:56 ./usr/bin/ -rwxr-xr-x root/root 1713356 2022-09-02 20:56 ./usr/bin/sga -rwxr-xr-x root/root 4508 2022-09-02 20:56 ./usr/bin/sga-align -rwxr-xr-x root/root 5734 2022-09-02 20:56 ./usr/bin/sga-astat -rwxr-xr-x root/root 3290 2022-09-02 20:56 ./usr/bin/sga-bam2de -rwxr-xr-x root/root 1873 2022-09-02 20:56 ./usr/bin/sga-mergeDriver drwxr-xr-x root/root 0 2022-09-02 20:56 ./usr/share/ drwxr-xr-x root/root 0 2022-09-02 20:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-09-02 20:56 ./usr/share/doc/sga/ -rw-r--r-- root/root 349 2021-09-17 13:53 ./usr/share/doc/sga/README.Debian -rw-r--r-- root/root 3280 2016-08-05 20:27 ./usr/share/doc/sga/README.gz -rw-r--r-- root/root 515 2016-08-05 20:27 ./usr/share/doc/sga/README.md -rw-r--r-- root/root 217 2022-09-02 20:56 ./usr/share/doc/sga/changelog.Debian.armel.gz -rw-r--r-- root/root 1268 2022-09-02 20:56 ./usr/share/doc/sga/changelog.Debian.gz -rw-r--r-- root/root 3396 2021-09-17 13:53 ./usr/share/doc/sga/copyright drwxr-xr-x root/root 0 2022-09-02 20:56 ./usr/share/doc/sga/examples/ -rw-r--r-- root/root 3312 2022-09-02 20:56 ./usr/share/doc/sga/examples/sga-celegans.sh -rw-r--r-- root/root 3391 2022-09-02 20:56 ./usr/share/doc/sga/index.html drwxr-xr-x root/root 0 2022-09-02 20:56 ./usr/share/man/ drwxr-xr-x root/root 0 2022-09-02 20:56 ./usr/share/man/man1/ -rw-r--r-- root/root 517 2022-09-02 20:56 ./usr/share/man/man1/sga-align.1.gz -rw-r--r-- root/root 656 2022-09-02 20:56 ./usr/share/man/man1/sga-astat.1.gz -rw-r--r-- root/root 523 2022-09-02 20:56 ./usr/share/man/man1/sga-bam2de.1.gz -rw-r--r-- root/root 328 2022-09-02 20:56 ./usr/share/man/man1/sga-mergeDriver.1.gz -rw-r--r-- root/root 1023 2022-09-02 20:56 ./usr/share/man/man1/sga.1.gz +------------------------------------------------------------------------------+ | Post Build Mon, 28 Jul 2025 23:01:13 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 28 Jul 2025 23:01:13 +0000 | +------------------------------------------------------------------------------+ Purging /build/sga-qoWx2H Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 28 Jul 2025 23:01:14 +0000 | +------------------------------------------------------------------------------+ Build Architecture: armel Build Type: any Build-Space: 296580 Build-Time: 126 Distribution: unstable Host Architecture: armel Install-Time: 5 Job: /srv/rebuilderd/tmp/rebuilderdR7kwFT/inputs/sga_0.10.15-7.dsc Machine Architecture: arm64 Package: sga Package-Time: 146 Source-Version: 0.10.15-7 Space: 296580 Status: successful Version: 0.10.15-7+b1 -------------------------------------------------------------------------------- Finished at 2025-07-28T23:01:09Z Build needed 00:02:26, 296580k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderdR7kwFT/out checking sga-dbgsym_0.10.15-7+b1_armel.deb: size... sha256... size differs for sga_0.10.15-7+b1_armel.deb md5... sha1... all OK checking sga_0.10.15-7+b1_armel.deb: