=============================================================================== 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/rebuilderdkZTweZ/inputs/bwa-mem2_2.3+ds-1_amd64.buildinfo Source: bwa-mem2 Version: 2.3+ds-1 rebuilderd-worker node: osuosl41-amd64 +------------------------------------------------------------------------------+ | Downloading sources Mon, 23 Feb 2026 18:14:33 +0000 | +------------------------------------------------------------------------------+ Get:1 https://deb.debian.org/debian trixie InRelease [140 kB] Get:2 https://deb.debian.org/debian-security trixie-security InRelease [43.4 kB] Get:3 https://deb.debian.org/debian trixie-updates InRelease [47.3 kB] Get:4 https://deb.debian.org/debian trixie-proposed-updates InRelease [57.6 kB] Get:5 https://deb.debian.org/debian trixie-backports InRelease [54.0 kB] Get:6 https://deb.debian.org/debian forky InRelease [137 kB] Get:7 https://deb.debian.org/debian sid InRelease [187 kB] Get:8 https://deb.debian.org/debian experimental InRelease [91.7 kB] Get:9 https://deb.debian.org/debian trixie/non-free-firmware Sources [6,552 B] Get:10 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:11 https://deb.debian.org/debian-security trixie-security/main Sources [136 kB] Get:12 https://deb.debian.org/debian-security trixie-security/non-free-firmware Sources [696 B] Get:13 https://deb.debian.org/debian trixie-updates/main Sources [2,788 B] Get:14 https://deb.debian.org/debian trixie-proposed-updates/main Sources [70.5 kB] Get:15 https://deb.debian.org/debian trixie-backports/main Sources [147 kB] Get:16 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [2,468 B] Get:17 https://deb.debian.org/debian forky/non-free-firmware Sources [8,304 B] Get:18 https://deb.debian.org/debian forky/main Sources [10.6 MB] Get:19 https://deb.debian.org/debian sid/non-free-firmware Sources [10.6 kB] Get:20 https://deb.debian.org/debian sid/main Sources [11.3 MB] Get:21 https://deb.debian.org/debian experimental/non-free-firmware Sources [2,572 B] Get:22 https://deb.debian.org/debian experimental/main Sources [403 kB] Fetched 34.0 MB in 3s (9,751 kB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/b/bwa-mem2/bwa-mem2_2.3%2bds-1.dsc' bwa-mem2_2.3+ds-1.dsc 2043 SHA256:e1e153d7f0d93cc29267b5da8a86307621ab66bbaa12dbdcea2a9301f212ae35 'https://deb.debian.org/debian/pool/main/b/bwa-mem2/bwa-mem2_2.3%2bds.orig.tar.xz' bwa-mem2_2.3+ds.orig.tar.xz 231664 SHA256:9b864d981d626f285d04aaedd7e37eff922e611b27fabee784db7d019fe9bb89 'https://deb.debian.org/debian/pool/main/b/bwa-mem2/bwa-mem2_2.3%2bds-1.debian.tar.xz' bwa-mem2_2.3+ds-1.debian.tar.xz 8300 SHA256:2a248b437a5385aa4ac8ba7eec70339128238ce6fdddebf7b645fc9c7f9826bb 9b864d981d626f285d04aaedd7e37eff922e611b27fabee784db7d019fe9bb89 bwa-mem2_2.3+ds.orig.tar.xz 2a248b437a5385aa4ac8ba7eec70339128238ce6fdddebf7b645fc9c7f9826bb bwa-mem2_2.3+ds-1.debian.tar.xz e1e153d7f0d93cc29267b5da8a86307621ab66bbaa12dbdcea2a9301f212ae35 bwa-mem2_2.3+ds-1.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Mon, 23 Feb 2026 18:14:37 +0000 | +------------------------------------------------------------------------------+ Rebuilding bwa-mem2=2.3+ds-1 in /srv/rebuilderd/tmp/rebuilderdkZTweZ/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdkZTweZ/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdkZTweZ/inputs/bwa-mem2_2.3+ds-1_amd64.buildinfo /srv/rebuilderd/tmp/rebuilderdkZTweZ/inputs/bwa-mem2_2.3+ds-1_amd64.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/bwa-mem2-2.3+ds I: verifying dsc... successful! Get:1 http://deb.debian.org/debian unstable InRelease [187 kB] Get:2 http://snapshot.debian.org/archive/debian/20260221T204712Z forky InRelease [137 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 Packages [10.2 MB] Get:4 http://snapshot.debian.org/archive/debian/20260221T204712Z forky/main amd64 Packages [9531 kB] Fetched 20.0 MB in 2s (11.9 MB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20260221T204712Z/dists/forky/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://deb.debian.org/debian unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.46-2 [1058 kB] Fetched 1058 kB in 0s (75.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpegtp1sx9/binutils-x86-64-linux-gnu_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libperl5.40 amd64 5.40.1-7 [4317 kB] Fetched 4317 kB in 0s (143 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp86lzq65_/libperl5.40_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.2-1 [1687 kB] Fetched 1687 kB in 0s (94.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpajk2jypk/gettext_0.23.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libctf0 amd64 2.46-2 [92.2 kB] Fetched 92.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnqdr_y7e/libctf0_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 coreutils amd64 9.7-3 [3024 kB] Fetched 3024 kB in 0s (122 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprv5wqiho/coreutils_9.7-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmpc3 amd64 1.3.1-2+b1 [52.2 kB] Fetched 52.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8_nu8bhv/libmpc3_1.3.1-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmd0 amd64 1.1.0-2+b2 [36.2 kB] Fetched 36.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdrjz61ie/libmd0_1.1.0-2+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 grep amd64 3.12-1 [443 kB] Fetched 443 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplk_bppeb/grep_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Fetched 19.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7dl5qcng/libfile-stripnondeterminism-perl_1.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsystemd0 amd64 259.1-1 [471 kB] Fetched 471 kB in 0s (46.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptry4dy76/libsystemd0_259.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.30 [942 kB] Fetched 942 kB in 0s (71.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_s8f56hw/debhelper_13.30_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblzma5 amd64 5.8.2-2 [327 kB] Fetched 327 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpavj1jzu1/liblzma5_5.8.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp amd64 4:15.2.0-5 [1564 B] Fetched 1564 B in 0s (0 B/s) dpkg-name: info: moved 'cpp_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpl4k0okm4/cpp_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl-modules-5.40 all 5.40.1-7 [3012 kB] Fetched 3012 kB in 0s (129 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpetin5a0_/perl-modules-5.40_5.40.1-7_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libsframe3 amd64 2.46-2 [84.6 kB] Fetched 84.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1ywkaga9/libsframe3_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtsan2 amd64 15.2.0-13 [2491 kB] Fetched 2491 kB in 0s (124 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2s60jme0/libtsan2_15.2.0-13_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260221T204712Z forky/main amd64 libmount1 amd64 2.41.3-3 [212 kB] Fetched 212 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvh5qd3u8/libmount1_2.41.3-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 linux-libc-dev all 6.18.12-1 [2574 kB] Fetched 2574 kB in 0s (122 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzl_bmm7i/linux-libc-dev_6.18.12-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sysvinit-utils amd64 3.15-6 [35.0 kB] Fetched 35.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0gom1zsx/sysvinit-utils_3.15-6_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5+b1 [561 kB] Fetched 561 kB in 0s (47.6 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp9uszku10/libgmp10_6.3.0+dfsg-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Fetched 63.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmfboq8ix/rpcsvc-proto_1.4.3-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libseccomp2 amd64 2.6.0-2+b1 [52.2 kB] Fetched 52.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqutglvwp/libseccomp2_2.6.0-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Fetched 8812 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsms_7eu8/dh-strip-nondeterminism_1.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libisl23 amd64 0.27-1+b1 [663 kB] Fetched 663 kB in 0s (55.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8b_6p8j4/libisl23_0.27-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Fetched 60.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwpfrdwk6/autotools-dev_20240727.1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgomp1 amd64 15.2.0-13 [141 kB] Fetched 141 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjlj2qbja/libgomp1_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcap2 amd64 1:2.75-10+b5 [28.8 kB] Fetched 28.8 kB in 0s (0 B/s) dpkg-name: info: moved 'libcap2_1%3a2.75-10+b5_amd64.deb' to '/srv/rebuilderd/tmp/tmp3xwoz74c/libcap2_2.75-10+b5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-5 [1436 B] Fetched 1436 B in 0s (0 B/s) dpkg-name: info: moved 'gcc-x86-64-linux-gnu_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpbw8xvahg/gcc-x86-64-linux-gnu_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules amd64 1.7.0-5+b1 [179 kB] Fetched 179 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3r5lst9i/libpam-modules_1.7.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libubsan1 amd64 15.2.0-13 [1108 kB] Fetched 1108 kB in 0s (81.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpftuboxko/libubsan1_15.2.0-13_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260221T204712Z forky/main amd64 libsmartcols1 amd64 2.41.3-3 [145 kB] Fetched 145 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjvvsq1jg/libsmartcols1_2.41.3-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 binutils-common amd64 2.46-2 [2635 kB] Fetched 2635 kB in 0s (119 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0io8l3xc/binutils-common_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libatomic1 amd64 15.2.0-13 [9492 B] Fetched 9492 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1yw6z0v0/libatomic1_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libaudit1 amd64 1:4.1.2-1+b1 [60.2 kB] Fetched 60.2 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit1_1%3a4.1.2-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpuwkxg9ye/libaudit1_4.1.2-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-base all 6.6+20251231-1 [277 kB] Fetched 277 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy5bvfkio/ncurses-base_6.6+20251231-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libjansson4 amd64 2.14-2+b4 [40.1 kB] Fetched 40.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnhckr9ke/libjansson4_2.14-2+b4_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-10 [1194 kB] Fetched 1194 kB in 0s (73.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6pg0wsee/groff-base_1.23.0-10_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2+b1 [466 kB] Fetched 466 kB in 0s (45.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxgtgqoh3/libunistring5_1.3-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libzstd1 amd64 1.5.7+dfsg-3+b1 [308 kB] Fetched 308 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf9k6zfrd/libzstd1_1.5.7+dfsg-3+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21+nmu1 [11.7 kB] Fetched 11.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplg5efrrw/dh-autoreconf_21+nmu1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 base-files amd64 14 [72.9 kB] Fetched 72.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz3qymrf1/base-files_14_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libacl1 amd64 2.3.2-3 [32.7 kB] Fetched 32.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp0h8fgv5/libacl1_2.3.2-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Fetched 216 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuzmpu6hw/po-debconf_1.0.22_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libstdc++6 amd64 15.2.0-13 [737 kB] Fetched 737 kB in 0s (57.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkioprayh/libstdc++6_15.2.0-13_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260221T204712Z forky/main amd64 util-linux amd64 2.41.3-3 [1167 kB] Fetched 1167 kB in 0s (83.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw5vm1sa5/util-linux_2.41.3-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbinutils amd64 2.46-2 [548 kB] Fetched 548 kB in 0s (46.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyyvatdt9/libbinutils_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++ amd64 4:15.2.0-5 [1344 B] Fetched 1344 B in 0s (0 B/s) dpkg-name: info: moved 'g++_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpwv6ai713/g++_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.30 [92.7 kB] Fetched 92.7 kB in 0s (8288 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpurc4tgnh/libdebhelper-perl_13.30_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 base-passwd amd64 3.6.8 [54.6 kB] Fetched 54.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzktp9nhh/base-passwd_3.6.8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libhwasan0 amd64 15.2.0-13 [1538 kB] Fetched 1538 kB in 0s (94.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoeypzx5t/libhwasan0_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libasan8 amd64 15.2.0-13 [2779 kB] Fetched 2779 kB in 0s (124 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpffj8o7ot/libasan8_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debconf all 1.5.92 [123 kB] Fetched 123 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpulo26f7x/debconf_1.5.92_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260221T204712Z forky/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Fetched 467 kB in 0s (12.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvroucsty/libsimde-dev_0.8.2-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libselinux1 amd64 3.9-4+b1 [86.1 kB] Fetched 86.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuptiwmxk/libselinux1_3.9-4+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bzip2 amd64 1.0.8-6+b1 [41.0 kB] Fetched 41.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpccqbg1zd/bzip2_1.0.8-6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 bash amd64 5.3-2 [1561 kB] Fetched 1561 kB in 0s (100 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphny0vmmd/bash_5.3-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-13 [23.4 MB] Fetched 23.4 MB in 0s (169 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj9r14_xk/gcc-15-x86-64-linux-gnu_15.2.0-13_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260221T204712Z forky/main amd64 tar amd64 1.35+dfsg-3.1 [815 kB] Fetched 815 kB in 0s (65.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyu17zfoi/tar_1.35+dfsg-3.1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dash amd64 0.5.12-12 [98.5 kB] Fetched 98.5 kB in 0s (1961 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpve5fwcwh/dash_0.5.12-12_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260221T204712Z forky/main amd64 libcap-ng0 amd64 0.8.5-4+b2 [17.5 kB] Fetched 17.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdnxabogc/libcap-ng0_0.8.5-4+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libitm1 amd64 15.2.0-13 [26.5 kB] Fetched 26.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8lrd9fn4/libitm1_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libctf-nobfd0 amd64 2.46-2 [160 kB] Fetched 160 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpffxxhyrs/libctf-nobfd0_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-8 [15.2 kB] Fetched 15.2 kB in 0s (770 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyqekz7a0/liblocale-gettext-perl_1.07-8_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Fetched 494 kB in 0s (42.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwk2h_wae/autoconf_2.72-3.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260221T204712Z forky/main amd64 libblkid1 amd64 2.41.3-3 [174 kB] Fetched 174 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuflt1t6q/libblkid1_2.41.3-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-5 [5324 B] Fetched 5324 B in 0s (0 B/s) dpkg-name: info: moved 'cpp-x86-64-linux-gnu_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpgvall5iy/cpp-x86-64-linux-gnu_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdebconfclient0 amd64 0.282+b2 [11.2 kB] Fetched 11.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp443todws/libdebconfclient0_0.282+b2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgdbm-compat4t64 amd64 1.26-1+b1 [53.1 kB] Fetched 53.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp846mj5gh/libgdbm-compat4t64_1.26-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 hostname amd64 3.25 [11.0 kB] Fetched 11.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprugtwrux/hostname_3.25_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-modules-bin amd64 1.7.0-5+b1 [49.8 kB] Fetched 49.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1wupjbbk/libpam-modules-bin_1.7.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 diffutils amd64 1:3.12-1 [405 kB] Fetched 405 kB in 0s (0 B/s) dpkg-name: info: moved 'diffutils_1%3a3.12-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp44vlpz92/diffutils_3.12-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 xz-utils amd64 5.8.2-2 [706 kB] Fetched 706 kB in 0s (65.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnc4gqo8x/xz-utils_5.8.2-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg amd64 1.23.5 [1527 kB] Fetched 1527 kB in 0s (103 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcxws14x5/dpkg_1.23.5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-dev-bin amd64 2.42-13 [61.5 kB] Fetched 61.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplq_2q90p/libc-dev-bin_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl-base amd64 5.40.1-7 [1679 kB] Fetched 1679 kB in 0s (109 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5p5_di3_/perl-base_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 liblsan0 amd64 15.2.0-13 [1249 kB] Fetched 1249 kB in 0s (81.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8ukwj9x9/liblsan0_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b1 [68.8 kB] Fetched 68.8 kB in 3s (23.1 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf_htl72s/libuchardet0_0.0.8-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Fetched 27.0 kB in 1s (27.9 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpce0uygwn/sensible-utils_0.0.26_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libudev1 amd64 259.1-1 [158 kB] Fetched 158 kB in 4s (44.1 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcayhgcb8/libudev1_259.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam0g amd64 1.7.0-5+b1 [70.4 kB] Fetched 70.4 kB in 12s (5858 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz2mvdnd7/libpam0g_1.7.0-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 findutils amd64 4.10.0-3 [700 kB] Fetched 700 kB in 0s (44.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjeghmy9l/findutils_4.10.0-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-2 [42.1 kB] Fetched 42.1 kB in 0s (660 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptz00ll6g/libpipeline1_1.5.8-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmpfr6 amd64 4.2.2-2+b1 [729 kB] Fetched 729 kB in 0s (60.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp76xix2_j/libmpfr6_4.2.2-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 make amd64 4.4.1-3 [463 kB] Fetched 463 kB in 0s (40.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp807c6di9/make_4.4.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Fetched 1469 kB in 0s (100 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpckugiyfy/man-db_2.13.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 openssl-provider-legacy amd64 3.5.5-1 [311 kB] Fetched 311 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpygtqmbj_/openssl-provider-legacy_3.5.5-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-15 amd64 15.2.0-13 [1276 B] Fetched 1276 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppy33wous/cpp-15_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc-gconv-modules-extra amd64 2.42-13 [1123 kB] Fetched 1123 kB in 0s (81.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6vko8ww9/libc-gconv-modules-extra_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.2-1 [772 kB] Fetched 772 kB in 0s (68.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa0u9i23a/autopoint_0.23.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Fetched 185 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_pq62h5z/libelf1t64_0.194-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-5 [1200 B] Fetched 1200 B in 0s (0 B/s) dpkg-name: info: moved 'g++-x86-64-linux-gnu_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpwekg897c/g++-x86-64-linux-gnu_15.2.0-5_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 build-essential amd64 12.12 [4624 B] Fetched 4624 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp41jun02p/build-essential_12.12_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 ncurses-bin amd64 6.6+20251231-1 [445 kB] Fetched 445 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpduufovj1/ncurses-bin_6.6+20251231-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dpkg-dev all 1.23.5 [1318 kB] Fetched 1318 kB in 0s (95.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphcalorqr/dpkg-dev_1.23.5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 patch amd64 2.8-2 [134 kB] Fetched 134 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp19ga93e5/patch_2.8-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5+b1 [43.8 kB] Fetched 43.8 kB in 0s (0 B/s) dpkg-name: info: moved 'file_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpiybgrgfv/file_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-11 [710 kB] Fetched 710 kB in 0s (65.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbtngdviq/libdb5.3t64_5.3.28+dfsg2-11_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libquadmath0 amd64 15.2.0-13 [145 kB] Fetched 145 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpce30yeoy/libquadmath0_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5+b1 [110 kB] Fetched 110 kB in 0s (0 B/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmprfc6ar5c/libmagic1t64_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcc1-0 amd64 15.2.0-13 [42.7 kB] Fetched 42.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo5_xo6pi/libcc1-0_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.2-1 [245 kB] Fetched 245 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8iqikvam/gettext-base_0.23.2-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-9 [540 kB] Fetched 540 kB in 0s (51.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqvdpfqmx/libtool_2.5.4-9_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-13 [13.2 MB] Fetched 13.2 MB in 0s (179 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxu93xkmj/g++-15-x86-64-linux-gnu_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 init-system-helpers all 1.69 [39.3 kB] Fetched 39.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpei10ykjp/init-system-helpers_1.69_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 sed amd64 4.9-2 [329 kB] Fetched 329 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpagzprcgl/sed_4.9-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Fetched 108 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfrp6zfj8/dwz_0.16-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260221T204712Z forky/main amd64 libuuid1 amd64 2.41.3-3 [39.0 kB] Fetched 39.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmply33sow5/libuuid1_2.41.3-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 g++-15 amd64 15.2.0-13 [26.0 kB] Fetched 26.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp96qcq3ka/g++-15_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgcc-s1 amd64 15.2.0-13 [71.5 kB] Fetched 71.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpee7k3qq4/libgcc-s1_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Fetched 332 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnrypcp0r/m4_1.4.21-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Fetched 198 kB in 0s (1134 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb6e7h_x1/help2man_1.49.3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libssl3t64 amd64 3.5.5-1 [2449 kB] Fetched 2449 kB in 0s (121 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp91_lvz3q/libssl3t64_3.5.5-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgdbm6t64 amd64 1.26-1+b1 [78.9 kB] Fetched 78.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3aoryetf/libgdbm6t64_1.26-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-13 [12.1 MB] Fetched 12.1 MB in 0s (187 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyhqzght6/cpp-15-x86-64-linux-gnu_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-3 [878 kB] Fetched 878 kB in 0s (75.1 MB/s) dpkg-name: info: moved 'automake_1%3a1.18.1-3_all.deb' to '/srv/rebuilderd/tmp/tmpn5xib59b/automake_1.18.1-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.1+dfsg-2+b1 [641 kB] Fetched 641 kB in 0s (56.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpos4o6l2n/libxml2-16_2.15.1+dfsg-2+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libaudit-common all 1:4.1.2-1 [14.3 kB] Fetched 14.3 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit-common_1%3a4.1.2-1_all.deb' to '/srv/rebuilderd/tmp/tmppeay3vsx/libaudit-common_4.1.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6-dev amd64 2.42-13 [2016 kB] Fetched 2016 kB in 0s (121 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcrbtpehh/libc6-dev_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gzip amd64 1.13-1 [138 kB] Fetched 138 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp62qxlen6/gzip_1.13-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libstdc++-15-dev amd64 15.2.0-13 [2446 kB] Fetched 2446 kB in 0s (123 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpopjeo5fj/libstdc++-15-dev_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzonsfky0/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 perl amd64 5.40.1-7 [267 kB] Fetched 267 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5joiri6y/perl_5.40.1-7_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Fetched 22.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdpqrgzfw/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-3 [89.0 kB] Fetched 89.0 kB in 0s (0 B/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.1-3_amd64.deb' to '/srv/rebuilderd/tmp/tmp1gzq_npi/zlib1g_1.3.dfsg+really1.3.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libc6 amd64 2.42-13 [1814 kB] Fetched 1814 kB in 0s (113 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxpbosrde/libc6_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libcrypt1 amd64 1:4.5.1-1 [98.0 kB] Fetched 98.0 kB in 0s (0 B/s) dpkg-name: info: moved 'libcrypt1_1%3a4.5.1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmptwk4nfnv/libcrypt1_4.5.1-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgcc-15-dev amd64 15.2.0-13 [2719 kB] Fetched 2719 kB in 0s (125 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprf0q91fj/libgcc-15-dev_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 mawk amd64 1.3.4.20260129-1 [143 kB] Fetched 143 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4dguvwla/mawk_1.3.4.20260129-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-3 [919 kB] Fetched 919 kB in 0s (64.2 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.1-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpsngna909/zlib1g-dev_1.3.dfsg+really1.3.1-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libtinfo6 amd64 6.6+20251231-1 [354 kB] Fetched 354 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp36h57ja6/libtinfo6_6.6+20251231-1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc amd64 4:15.2.0-5 [5160 B] Fetched 5160 B in 0s (0 B/s) dpkg-name: info: moved 'gcc_4%3a15.2.0-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp50rkhvd_/gcc_15.2.0-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260221T204712Z forky/main amd64 bsdextrautils amd64 2.41.3-3 [99.1 kB] Fetched 99.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprqvnal10/bsdextrautils_2.41.3-3_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15-base amd64 15.2.0-13 [54.8 kB] Fetched 54.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzcswbf1_/gcc-15-base_15.2.0-13_amd64.deb' Downloading dependency 1 of 144: binutils-x86-64-linux-gnu:amd64=2.46-2 Downloading dependency 2 of 144: libperl5.40:amd64=5.40.1-7 Downloading dependency 3 of 144: gettext:amd64=0.23.2-1 Downloading dependency 4 of 144: libctf0:amd64=2.46-2 Downloading dependency 5 of 144: coreutils:amd64=9.7-3 Downloading dependency 6 of 144: libmpc3:amd64=1.3.1-2+b1 Downloading dependency 7 of 144: libmd0:amd64=1.1.0-2+b2 Downloading dependency 8 of 144: grep:amd64=3.12-1 Downloading dependency 9 of 144: libfile-stripnondeterminism-perl:amd64=1.15.0-1 Downloading dependency 10 of 144: libsystemd0:amd64=259.1-1 Downloading dependency 11 of 144: debhelper:amd64=13.30 Downloading dependency 12 of 144: liblzma5:amd64=5.8.2-2 Downloading dependency 13 of 144: cpp:amd64=4:15.2.0-5 Downloading dependency 14 of 144: perl-modules-5.40:amd64=5.40.1-7 Downloading dependency 15 of 144: libsframe3:amd64=2.46-2 Downloading dependency 16 of 144: libtsan2:amd64=15.2.0-13 Downloading dependency 17 of 144: libmount1:amd64=2.41.3-3 Downloading dependency 18 of 144: linux-libc-dev:amd64=6.18.12-1 Downloading dependency 19 of 144: sysvinit-utils:amd64=3.15-6 Downloading dependency 20 of 144: libgmp10:amd64=2:6.3.0+dfsg-5+b1 Downloading dependency 21 of 144: rpcsvc-proto:amd64=1.4.3-1 Downloading dependency 22 of 144: libseccomp2:amd64=2.6.0-2+b1 Downloading dependency 23 of 144: dh-strip-nondeterminism:amd64=1.15.0-1 Downloading dependency 24 of 144: libisl23:amd64=0.27-1+b1 Downloading dependency 25 of 144: autotools-dev:amd64=20240727.1 Downloading dependency 26 of 144: libgomp1:amd64=15.2.0-13 Downloading dependency 27 of 144: libcap2:amd64=1:2.75-10+b5 Downloading dependency 28 of 144: gcc-x86-64-linux-gnu:amd64=4:15.2.0-5 Downloading dependency 29 of 144: libpam-modules:amd64=1.7.0-5+b1 Downloading dependency 30 of 144: libubsan1:amd64=15.2.0-13 Downloading dependency 31 of 144: libsmartcols1:amd64=2.41.3-3 Downloading dependency 32 of 144: binutils-common:amd64=2.46-2 Downloading dependency 33 of 144: libatomic1:amd64=15.2.0-13 Downloading dependency 34 of 144: libaudit1:amd64=1:4.1.2-1+b1 Downloading dependency 35 of 144: ncurses-base:amd64=6.6+20251231-1 Downloading dependency 36 of 144: libjansson4:amd64=2.14-2+b4 Downloading dependency 37 of 144: groff-base:amd64=1.23.0-10 Downloading dependency 38 of 144: libunistring5:amd64=1.3-2+b1 Downloading dependency 39 of 144: libzstd1:amd64=1.5.7+dfsg-3+b1 Downloading dependency 40 of 144: dh-autoreconf:amd64=21+nmu1 Downloading dependency 41 of 144: base-files:amd64=14 Downloading dependency 42 of 144: libacl1:amd64=2.3.2-3 Downloading dependency 43 of 144: po-debconf:amd64=1.0.22 Downloading dependency 44 of 144: libstdc++6:amd64=15.2.0-13 Downloading dependency 45 of 144: util-linux:amd64=2.41.3-3 Downloading dependency 46 of 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dependency 63 of 144: liblocale-gettext-perl:amd64=1.07-8 Downloading dependency 64 of 144: autoconf:amd64=2.72-3.1 Downloading dependency 65 of 144: libblkid1:amd64=2.41.3-3 Downloading dependency 66 of 144: cpp-x86-64-linux-gnu:amd64=4:15.2.0-5 Downloading dependency 67 of 144: libdebconfclient0:amd64=0.282+b2 Downloading dependency 68 of 144: libgdbm-compat4t64:amd64=1.26-1+b1 Downloading dependency 69 of 144: hostname:amd64=3.25 Downloading dependency 70 of 144: libpam-modules-bin:amd64=1.7.0-5+b1 Downloading dependency 71 of 144: diffutils:amd64=1:3.12-1 Downloading dependency 72 of 144: xz-utils:amd64=5.8.2-2 Downloading dependency 73 of 144: dpkg:amd64=1.23.5 Downloading dependency 74 of 144: libc-dev-bin:amd64=2.42-13 Downloading dependency 75 of 144: perl-base:amd64=5.40.1-7 Downloading dependency 76 of 144: liblsan0:amd64=15.2.0-13 Downloading dependency 77 of 144: libuchardet0:amd64=0.0.8-2+b1 Downloading dependency 78 of 144: sensible-utils:amd64=0.0.26 Downloading dependency 79 of 144: libudev1:amd64=259.1-1 Downloading dependency 80 of 144: libpam0g:amd64=1.7.0-5+b1 Downloading dependency 81 of 144: findutils:amd64=4.10.0-3 Downloading dependency 82 of 144: libpipeline1:amd64=1.5.8-2 Downloading dependency 83 of 144: libmpfr6:amd64=4.2.2-2+b1 Downloading dependency 84 of 144: make:amd64=4.4.1-3 Downloading dependency 85 of 144: man-db:amd64=2.13.1-1 Downloading dependency 86 of 144: openssl-provider-legacy:amd64=3.5.5-1 Downloading dependency 87 of 144: cpp-15:amd64=15.2.0-13 Downloading dependency 88 of 144: libc-gconv-modules-extra:amd64=2.42-13 Downloading dependency 89 of 144: autopoint:amd64=0.23.2-1 Downloading dependency 90 of 144: libelf1t64:amd64=0.194-1 Downloading dependency 91 of 144: g++-x86-64-linux-gnu:amd64=4:15.2.0-5 Downloading dependency 92 of 144: build-essential:amd64=12.12 Downloading dependency 93 of 144: ncurses-bin:amd64=6.6+20251231-1 Downloading dependency 94 of 144: dpkg-dev:amd64=1.23.5 Downloading dependency 95 of 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dependency 112 of 144: libssl3t64:amd64=3.5.5-1 Downloading dependency 113 of 144: libgdbm6t64:amd64=1.26-1+b1 Downloading dependency 114 of 144: cpp-15-x86-64-linux-gnu:amd64=15.2.0-13 Downloading dependency 115 of 144: automake:amd64=1:1.18.1-3 Downloading dependency 116 of 144: libxml2-16:amd64=2.15.1+dfsg-2+b1 Downloading dependency 117 of 144: libaudit-common:amd64=1:4.1.2-1 Downloading dependency 118 of 144: libc6-dev:amd64=2.42-13 Downloading dependency 119 of 144: gzip:amd64=1.13-1 Downloading dependency 120 of 144: libstdc++-15-dev:amd64=15.2.0-13 Downloading dependency 121 of 144: libarchive-zip-perl:amd64=1.68-1 Downloading dependency 122 of 144: perl:amd64=5.40.1-7 Downloading dependency 123 of 144: intltool-debian:amd64=0.35.0+20060710.6 Downloading dependency 124 of 144: zlib1g:amd64=1:1.3.dfsg+really1.3.1-3 Downloading dependency 125 of 144: libc6:amd64=2.42-13 Downloading dependency 126 of 144: libcrypt1:amd64=1:4.5.1-1 Downloading dependency 127 of 144: libgcc-15-dev:amd64=15.2.0-13 Downloading dependency 128 of 144: mawk:amd64=1.3.4.20260129-1 Downloading dependency 129 of 144: zlib1g-dev:amd64=1:1.3.dfsg+really1.3.1-3 Downloading dependency 130 of 144: libtinfo6:amd64=6.6+20251231-1 Downloading dependency 131 of 144: gcc:amd64=4:15.2.0-5 Downloading dependency 132 of 144: bsdextrautils:amd64=2.41.3-3 Downloading dependency 133 of 144: gcc-15-base:amd64=15.2.0-13 Downloading dependency 134 of 144: libc-bin:amd64=2.42-13Get:1 http://deb.debian.org/debian unstable/main amd64 libc-bin amd64 2.42-13 [644 kB] Fetched 644 kB in 0s (59.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzozi50vm/libc-bin_2.42-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpam-runtime all 1.7.0-5 [249 kB] Fetched 249 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc88d2eu3/libpam-runtime_1.7.0-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libpcre2-8-0 amd64 10.46-1+b1 [298 kB] Fetched 298 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfgat_2w4/libpcre2-8-0_10.46-1+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 gcc-15 amd64 15.2.0-13 [535 kB] Fetched 535 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppkfct5fx/gcc-15_15.2.0-13_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libgprofng0 amd64 2.46-2 [820 kB] Fetched 820 kB in 0s (69.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaqt5gn54/libgprofng0_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libbz2-1.0 amd64 1.0.8-6+b1 [40.4 kB] Fetched 40.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptwj2twei/libbz2-1.0_1.0.8-6+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5+b1 [338 kB] Fetched 338 kB in 0s (0 B/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.46-5+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmprwe20t6c/libmagic-mgc_5.46-5+b1_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 debianutils amd64 5.23.2 [92.4 kB] Fetched 92.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwnne45ut/debianutils_5.23.2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libdpkg-perl all 1.23.5 [668 kB] Fetched 668 kB in 0s (62.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqh6vz2k3/libdpkg-perl_1.23.5_all.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 binutils amd64 2.46-2 [282 kB] Fetched 282 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmqksi4yp/binutils_2.46-2_amd64.deb' Get:1 http://deb.debian.org/debian unstable/main amd64 libattr1 amd64 1:2.5.2-4 [23.0 kB] Fetched 23.0 kB in 0s (0 B/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpyttqhig5/libattr1_2.5.2-4_amd64.deb' dpkg-buildpackage: info: source package debootsnap-dummy dpkg-buildpackage: info: source version 1.0 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Equivs Dummy Package Generator dpkg-buildpackage: info: host architecture amd64 dpkg-source --before-build . debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/debootsnap-dummy/ dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'debootsnap-dummy' in '../debootsnap-dummy_1.0_all.deb'. dpkg-genbuildinfo --build=binary -O../debootsnap-dummy_1.0_amd64.buildinfo dpkg-genchanges --build=binary -O../debootsnap-dummy_1.0_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) The package has been created. Attention, the package has been created in the /srv/rebuilderd/tmp/tmpt9xt7lp2/cache directory, not in ".." as indicated by the message above! I: automatically chosen mode: unshare I: chroot architecture amd64 is equal to the host's architecture I: using /srv/rebuilderd/tmp/mmdebstrap.0HT96L4ZSl as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.0HT96L4ZSl 127.0.0.1 - - [23/Feb/2026 18:15:58] code 404, message File not found 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:36905 ./ InRelease 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:36905 ./ Release [462 B] 127.0.0.1 - - [23/Feb/2026 18:15:58] code 404, message File not found 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:36905 ./ Release.gpg 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:36905 ./ Packages [176 kB] Fetched 177 kB in 0s (13.1 MB/s) Reading package lists... usr-is-merged found but not real -- not running merged-usr setup hook I: skipping apt-get update because it was already run I: downloading packages with apt... 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./gcc-15-base_15.2.0-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libc-gconv-modules-extra_2.42-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libc6_2.42-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libgcc-s1_15.2.0-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./mawk_1.3.4.20260129-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./base-files_14_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libtinfo6_6.6%2b20251231-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./debianutils_5.23.2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./bash_5.3-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libacl1_2.3.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libattr1_2.5.2-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libcap2_2.75-10%2bb5_amd64.deb HTTP/1.1" 200 - 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127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./sed_4.9-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libaudit-common_4.1.2-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libcap-ng0_0.8.5-4%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libaudit1_4.1.2-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libdb5.3t64_5.3.28%2bdfsg2-11_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./debconf_1.5.92_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libpam0g_1.7.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libpam-modules-bin_1.7.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libpam-modules_1.7.0-5%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libpam-runtime_1.7.0-5_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libblkid1_2.41.3-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libmount1_2.41.3-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libsmartcols1_2.41.3-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libudev1_259.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libuuid1_2.41.3-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./util-linux_2.41.3-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libdebconfclient0_0.282%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./base-passwd_3.6.8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./init-system-helpers_1.69_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./libc-bin_2.42-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./ncurses-base_6.6%2b20251231-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:15:58] "GET /./sysvinit-utils_3.15-6_amd64.deb HTTP/1.1" 200 - I: extracting archives... I: running --extract-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/extract00.sh /srv/rebuilderd/tmp/mmdebstrap.0HT96L4ZSl 127.0.0.1 - - [23/Feb/2026 18:15:59] code 404, message File not found 127.0.0.1 - - [23/Feb/2026 18:15:59] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:36905 ./ InRelease 127.0.0.1 - - [23/Feb/2026 18:15:59] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:36905 ./ Release 127.0.0.1 - - [23/Feb/2026 18:15:59] code 404, message File not found 127.0.0.1 - - [23/Feb/2026 18:15:59] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:36905 ./ Release.gpg Reading package lists... usr-is-merged found but not real -- not running merged-usr extract hook I: installing essential packages... I: running --essential-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/essential00.sh /srv/rebuilderd/tmp/mmdebstrap.0HT96L4ZSl usr-is-merged was not installed in a previous hook -- not running merged-usr essential hook I: installing remaining packages inside the chroot... 127.0.0.1 - - [23/Feb/2026 18:16:10] "GET /./liblocale-gettext-perl_1.07-8_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:16:10] "GET /./sensible-utils_0.0.26_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:16:10] "GET /./libstdc%2b%2b6_15.2.0-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:16:10] "GET /./libuchardet0_0.0.8-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:16:10] "GET /./groff-base_1.23.0-10_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:16:10] "GET /./bsdextrautils_2.41.3-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:16:10] "GET /./libgdbm6t64_1.26-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:16:10] "GET /./libpipeline1_1.5.8-2_amd64.deb HTTP/1.1" 200 - 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127.0.0.1 - - [23/Feb/2026 18:16:11] "GET /./zlib1g-dev_1.3.dfsg%2breally1.3.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Feb/2026 18:16:11] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmpt9xt7lp2/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.0HT96L4ZSl Reading package lists... Building dependency tree... Reading state information... binutils-x86-64-linux-gnu is already the newest version (2.46-2). binutils-x86-64-linux-gnu set to manually installed. libperl5.40 is already the newest version (5.40.1-7). libperl5.40 set to manually installed. gettext is already the newest version (0.23.2-1). gettext set to manually installed. libctf0 is already the newest version (2.46-2). libctf0 set to manually installed. coreutils is already the newest version (9.7-3). libmpc3 is already the newest version (1.3.1-2+b1). libmpc3 set to manually installed. libmd0 is already the newest version (1.1.0-2+b2). grep is already the newest version (3.12-1). libfile-stripnondeterminism-perl is already the newest version (1.15.0-1). libfile-stripnondeterminism-perl set to manually installed. libsystemd0 is already the newest version (259.1-1). debhelper is already the newest version (13.30). debhelper set to manually installed. liblzma5 is already the newest version (5.8.2-2). cpp is already the newest version (4:15.2.0-5). cpp set to manually installed. perl-modules-5.40 is already the newest version (5.40.1-7). perl-modules-5.40 set to manually installed. libsframe3 is already the newest version (2.46-2). libsframe3 set to manually installed. libtsan2 is already the newest version (15.2.0-13). libtsan2 set to manually installed. libmount1 is already the newest version (2.41.3-3). linux-libc-dev is already the newest version (6.18.12-1). linux-libc-dev set to manually installed. sysvinit-utils is already the newest version (3.15-6). libgmp10 is already the newest version (2:6.3.0+dfsg-5+b1). rpcsvc-proto is already the newest version (1.4.3-1). rpcsvc-proto set to manually installed. libseccomp2 is already the newest version (2.6.0-2+b1). libseccomp2 set to manually installed. dh-strip-nondeterminism is already the newest version (1.15.0-1). dh-strip-nondeterminism set to manually installed. libisl23 is already the newest version (0.27-1+b1). libisl23 set to manually installed. autotools-dev is already the newest version (20240727.1). autotools-dev set to manually installed. libgomp1 is already the newest version (15.2.0-13). libgomp1 set to manually installed. libcap2 is already the newest version (1:2.75-10+b5). gcc-x86-64-linux-gnu is already the newest version (4:15.2.0-5). gcc-x86-64-linux-gnu set to manually installed. libpam-modules is already the newest version (1.7.0-5+b1). libubsan1 is already the newest version (15.2.0-13). libubsan1 set to manually installed. libsmartcols1 is already the newest version (2.41.3-3). binutils-common is already the newest version (2.46-2). binutils-common set to manually installed. libatomic1 is already the newest version (15.2.0-13). libatomic1 set to manually installed. libaudit1 is already the newest version (1:4.1.2-1+b1). ncurses-base is already the newest version (6.6+20251231-1). libjansson4 is already the newest version (2.14-2+b4). libjansson4 set to manually installed. groff-base is already the newest version (1.23.0-10). groff-base set to manually installed. libunistring5 is already the newest version (1.3-2+b1). libunistring5 set to manually installed. libzstd1 is already the newest version (1.5.7+dfsg-3+b1). dh-autoreconf is already the newest version (21+nmu1). dh-autoreconf set to manually installed. base-files is already the newest version (14). libacl1 is already the newest version (2.3.2-3). po-debconf is already the newest version (1.0.22). po-debconf set to manually installed. libstdc++6 is already the newest version (15.2.0-13). libstdc++6 set to manually installed. util-linux is already the newest version (2.41.3-3). libbinutils is already the newest version (2.46-2). libbinutils set to manually installed. g++ is already the newest version (4:15.2.0-5). g++ set to manually installed. libdebhelper-perl is already the newest version (13.30). libdebhelper-perl set to manually installed. base-passwd is already the newest version (3.6.8). libhwasan0 is already the newest version (15.2.0-13). libhwasan0 set to manually installed. libasan8 is already the newest version (15.2.0-13). libasan8 set to manually installed. debconf is already the newest version (1.5.92). libsimde-dev is already the newest version (0.8.2-3). libsimde-dev set to manually installed. libselinux1 is already the newest version (3.9-4+b1). bzip2 is already the newest version (1.0.8-6+b1). bzip2 set to manually installed. bash is already the newest version (5.3-2). gcc-15-x86-64-linux-gnu is already the newest version (15.2.0-13). gcc-15-x86-64-linux-gnu set to manually installed. tar is already the newest version (1.35+dfsg-3.1). dash is already the newest version (0.5.12-12). libcap-ng0 is already the newest version (0.8.5-4+b2). libitm1 is already the newest version (15.2.0-13). libitm1 set to manually installed. libctf-nobfd0 is already the newest version (2.46-2). libctf-nobfd0 set to manually installed. liblocale-gettext-perl is already the newest version (1.07-8). liblocale-gettext-perl set to manually installed. autoconf is already the newest version (2.72-3.1). autoconf set to manually installed. libblkid1 is already the newest version (2.41.3-3). cpp-x86-64-linux-gnu is already the newest version (4:15.2.0-5). cpp-x86-64-linux-gnu set to manually installed. libdebconfclient0 is already the newest version (0.282+b2). libgdbm-compat4t64 is already the newest version (1.26-1+b1). libgdbm-compat4t64 set to manually installed. hostname is already the newest version (3.25). libpam-modules-bin is already the newest version (1.7.0-5+b1). diffutils is already the newest version (1:3.12-1). xz-utils is already the newest version (5.8.2-2). xz-utils set to manually installed. dpkg is already the newest version (1.23.5). libc-dev-bin is already the newest version (2.42-13). libc-dev-bin set to manually installed. perl-base is already the newest version (5.40.1-7). liblsan0 is already the newest version (15.2.0-13). liblsan0 set to manually installed. libuchardet0 is already the newest version (0.0.8-2+b1). libuchardet0 set to manually installed. sensible-utils is already the newest version (0.0.26). sensible-utils set to manually installed. libudev1 is already the newest version (259.1-1). libpam0g is already the newest version (1.7.0-5+b1). findutils is already the newest version (4.10.0-3). libpipeline1 is already the newest version (1.5.8-2). libpipeline1 set to manually installed. libmpfr6 is already the newest version (4.2.2-2+b1). libmpfr6 set to manually installed. make is already the newest version (4.4.1-3). make set to manually installed. man-db is already the newest version (2.13.1-1). man-db set to manually installed. openssl-provider-legacy is already the newest version (3.5.5-1). cpp-15 is already the newest version (15.2.0-13). cpp-15 set to manually installed. libc-gconv-modules-extra is already the newest version (2.42-13). autopoint is already the newest version (0.23.2-1). autopoint set to manually installed. libelf1t64 is already the newest version (0.194-1). libelf1t64 set to manually installed. g++-x86-64-linux-gnu is already the newest version (4:15.2.0-5). g++-x86-64-linux-gnu set to manually installed. build-essential is already the newest version (12.12). build-essential set to manually installed. ncurses-bin is already the newest version (6.6+20251231-1). dpkg-dev is already the newest version (1.23.5). dpkg-dev set to manually installed. patch is already the newest version (2.8-2). patch set to manually installed. file is already the newest version (1:5.46-5+b1). file set to manually installed. libdb5.3t64 is already the newest version (5.3.28+dfsg2-11). libquadmath0 is already the newest version (15.2.0-13). libquadmath0 set to manually installed. libmagic1t64 is already the newest version (1:5.46-5+b1). libmagic1t64 set to manually installed. libcc1-0 is already the newest version (15.2.0-13). libcc1-0 set to manually installed. gettext-base is already the newest version (0.23.2-1). gettext-base set to manually installed. libtool is already the newest version (2.5.4-9). libtool set to manually installed. g++-15-x86-64-linux-gnu is already the newest version (15.2.0-13). g++-15-x86-64-linux-gnu set to manually installed. init-system-helpers is already the newest version (1.69). sed is already the newest version (4.9-2). dwz is already the newest version (0.16-2). dwz set to manually installed. libuuid1 is already the newest version (2.41.3-3). g++-15 is already the newest version (15.2.0-13). g++-15 set to manually installed. libgcc-s1 is already the newest version (15.2.0-13). m4 is already the newest version (1.4.21-1). m4 set to manually installed. help2man is already the newest version (1.49.3). help2man set to manually installed. libssl3t64 is already the newest version (3.5.5-1). libgdbm6t64 is already the newest version (1.26-1+b1). libgdbm6t64 set to manually installed. cpp-15-x86-64-linux-gnu is already the newest version (15.2.0-13). cpp-15-x86-64-linux-gnu set to manually installed. automake is already the newest version (1:1.18.1-3). automake set to manually installed. libxml2-16 is already the newest version (2.15.1+dfsg-2+b1). libxml2-16 set to manually installed. libaudit-common is already the newest version (1:4.1.2-1). libc6-dev is already the newest version (2.42-13). libc6-dev set to manually installed. gzip is already the newest version (1.13-1). libstdc++-15-dev is already the newest version (15.2.0-13). libstdc++-15-dev set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. perl is already the newest version (5.40.1-7). perl set to manually installed. intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.1-3). libc6 is already the newest version (2.42-13). libcrypt1 is already the newest version (1:4.5.1-1). libgcc-15-dev is already the newest version (15.2.0-13). libgcc-15-dev set to manually installed. mawk is already the newest version (1.3.4.20260129-1). zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.1-3). zlib1g-dev set to manually installed. libtinfo6 is already the newest version (6.6+20251231-1). gcc is already the newest version (4:15.2.0-5). gcc set to manually installed. bsdextrautils is already the newest version (2.41.3-3). bsdextrautils set to manually installed. gcc-15-base is already the newest version (15.2.0-13). libc-bin is already the newest version (2.42-13). libpam-runtime is already the newest version (1.7.0-5). libpcre2-8-0 is already the newest version (10.46-1+b1). gcc-15 is already the newest version (15.2.0-13). gcc-15 set to manually installed. libgprofng0 is already the newest version (2.46-2). libgprofng0 set to manually installed. libbz2-1.0 is already the newest version (1.0.8-6+b1). libmagic-mgc is already the newest version (1:5.46-5+b1). libmagic-mgc set to manually installed. debianutils is already the newest version (5.23.2). libdpkg-perl is already the newest version (1.23.5). libdpkg-perl set to manually installed. binutils is already the newest version (2.46-2). binutils set to manually installed. libattr1 is already the newest version (1:2.5.2-4). 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.0HT96L4ZSl (Reading database ... 14110 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.0HT96L4ZSl I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.0HT96L4ZSl 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.0HT96L4ZSl... I: success in 31.0760 seconds Downloading dependency 135 of 144: libpam-runtime:amd64=1.7.0-5 Downloading dependency 136 of 144: libpcre2-8-0:amd64=10.46-1+b1 Downloading dependency 137 of 144: gcc-15:amd64=15.2.0-13 Downloading dependency 138 of 144: libgprofng0:amd64=2.46-2 Downloading dependency 139 of 144: libbz2-1.0:amd64=1.0.8-6+b1 Downloading dependency 140 of 144: libmagic-mgc:amd64=1:5.46-5+b1 Downloading dependency 141 of 144: debianutils:amd64=5.23.2 Downloading dependency 142 of 144: libdpkg-perl:amd64=1.23.5 Downloading dependency 143 of 144: binutils:amd64=2.46-2 Downloading dependency 144 of 144: libattr1:amd64=1:2.5.2-4 env --chdir=/srv/rebuilderd/tmp/rebuilderdkZTweZ/out DEB_BUILD_OPTIONS=parallel=6 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1771672728 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildU3O6XM/debrebuild.sbuildrc.5c3tIgRcayNo sbuild --build=amd64 --host=amd64 --no-source --arch-any --no-arch-all --chroot=/srv/rebuilderd/tmp/debrebuildU3O6XM/debrebuild.tar._wncqzifuw5L --chroot-mode=unshare --dist=unstable --no-run-lintian --no-run-piuparts --no-run-autopkgtest --no-apt-update --no-apt-upgrade --no-apt-distupgrade --verbose --nolog --bd-uninstallable-explainer= --build-path=/build/reproducible-path --dsc-dir=bwa-mem2-2.3+ds /srv/rebuilderd/tmp/rebuilderdkZTweZ/inputs/bwa-mem2_2.3+ds-1.dsc I: consider moving your ~/.sbuildrc to /srv/rebuilderd/.config/sbuild/config.pl The Debian buildds switched to the "unshare" backend and sbuild will default to it in the future. To start using "unshare" add this to your `~/.config/sbuild/config.pl`: $chroot_mode = "unshare"; If you want to keep the old "schroot" mode even in the future, add the following to your `~/.config/sbuild/config.pl`: $chroot_mode = "schroot"; $schroot = "schroot"; sbuild (Debian sbuild) 0.89.3+deb13u4 (28 December 2025) on osuosl41-amd64.novalocal +==============================================================================+ | bwa-mem2 2.3+ds-1 (amd64) Mon, 23 Feb 2026 18:16:29 +0000 | +==============================================================================+ Package: bwa-mem2 Version: 2.3+ds-1 Source Version: 2.3+ds-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/rebuilderd/tmp/debrebuildU3O6XM/debrebuild.tar._wncqzifuw5L to /srv/rebuilderd/tmp/tmp.sbuild.TIyR5Zj52N... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Mon, 23 Feb 2026 18:16:33 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdkZTweZ/inputs/bwa-mem2_2.3+ds-1.dsc exists in /srv/rebuilderd/tmp/rebuilderdkZTweZ/inputs; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 23 Feb 2026 18:16:34 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libsimde-dev, help2man, build-essential Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libsimde-dev, help2man, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-o5awf0/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Mon, 23 Feb 2026 18:16:36 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Mon, 23 Feb 2026 18:16:37 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.73+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.73-1 (2026-02-17) amd64 (x86_64) Toolchain package versions: binutils_2.46-2 dpkg-dev_1.23.5 g++-15_15.2.0-13 gcc-15_15.2.0-13 libc6-dev_2.42-13 libstdc++-15-dev_15.2.0-13 libstdc++6_15.2.0-13 linux-libc-dev_6.18.12-1 Package versions: autoconf_2.72-3.1 automake_1:1.18.1-3 autopoint_0.23.2-1 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8 bash_5.3-2 binutils_2.46-2 binutils-common_2.46-2 binutils-x86-64-linux-gnu_2.46-2 bsdextrautils_2.41.3-3 build-essential_12.12 bzip2_1.0.8-6+b1 coreutils_9.7-3 cpp_4:15.2.0-5 cpp-15_15.2.0-13 cpp-15-x86-64-linux-gnu_15.2.0-13 cpp-x86-64-linux-gnu_4:15.2.0-5 dash_0.5.12-12 debconf_1.5.92 debhelper_13.30 debianutils_5.23.2 dh-autoreconf_21+nmu1 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 dpkg_1.23.5 dpkg-dev_1.23.5 dwz_0.16-2 file_1:5.46-5+b1 findutils_4.10.0-3 g++_4:15.2.0-5 g++-15_15.2.0-13 g++-15-x86-64-linux-gnu_15.2.0-13 g++-x86-64-linux-gnu_4:15.2.0-5 gcc_4:15.2.0-5 gcc-15_15.2.0-13 gcc-15-base_15.2.0-13 gcc-15-x86-64-linux-gnu_15.2.0-13 gcc-x86-64-linux-gnu_4:15.2.0-5 gettext_0.23.2-1 gettext-base_0.23.2-1 grep_3.12-1 groff-base_1.23.0-10 gzip_1.13-1 help2man_1.49.3 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-3 libarchive-zip-perl_1.68-1 libasan8_15.2.0-13 libatomic1_15.2.0-13 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46-2 libblkid1_2.41.3-3 libbz2-1.0_1.0.8-6+b1 libc-bin_2.42-13 libc-dev-bin_2.42-13 libc-gconv-modules-extra_2.42-13 libc6_2.42-13 libc6-dev_2.42-13 libcap-ng0_0.8.5-4+b2 libcap2_1:2.75-10+b5 libcc1-0_15.2.0-13 libcrypt1_1:4.5.1-1 libctf-nobfd0_2.46-2 libctf0_2.46-2 libdb5.3t64_5.3.28+dfsg2-11 libdebconfclient0_0.282+b2 libdebhelper-perl_13.30 libdpkg-perl_1.23.5 libelf1t64_0.194-1 libfile-stripnondeterminism-perl_1.15.0-1 libgcc-15-dev_15.2.0-13 libgcc-s1_15.2.0-13 libgdbm-compat4t64_1.26-1+b1 libgdbm6t64_1.26-1+b1 libgmp10_2:6.3.0+dfsg-5+b1 libgomp1_15.2.0-13 libgprofng0_2.46-2 libhwasan0_15.2.0-13 libisl23_0.27-1+b1 libitm1_15.2.0-13 libjansson4_2.14-2+b4 liblocale-gettext-perl_1.07-8 liblsan0_15.2.0-13 liblzma5_5.8.2-2 libmagic-mgc_1:5.46-5+b1 libmagic1t64_1:5.46-5+b1 libmd0_1.1.0-2+b2 libmount1_2.41.3-3 libmpc3_1.3.1-2+b1 libmpfr6_4.2.2-2+b1 libpam-modules_1.7.0-5+b1 libpam-modules-bin_1.7.0-5+b1 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5+b1 libpcre2-8-0_10.46-1+b1 libperl5.40_5.40.1-7 libpipeline1_1.5.8-2 libquadmath0_15.2.0-13 libseccomp2_2.6.0-2+b1 libselinux1_3.9-4+b1 libsframe3_2.46-2 libsimde-dev_0.8.2-3 libsmartcols1_2.41.3-3 libssl3t64_3.5.5-1 libstdc++-15-dev_15.2.0-13 libstdc++6_15.2.0-13 libsystemd0_259.1-1 libtinfo6_6.6+20251231-1 libtool_2.5.4-9 libtsan2_15.2.0-13 libubsan1_15.2.0-13 libuchardet0_0.0.8-2+b1 libudev1_259.1-1 libunistring5_1.3-2+b1 libuuid1_2.41.3-3 libxml2-16_2.15.1+dfsg-2+b1 libzstd1_1.5.7+dfsg-3+b1 linux-libc-dev_6.18.12-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260129-1 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1 openssl-provider-legacy_3.5.5-1 patch_2.8-2 perl_5.40.1-7 perl-base_5.40.1-7 perl-modules-5.40_5.40.1-7 po-debconf_1.0.22 rpcsvc-proto_1.4.3-1 sed_4.9-2 sensible-utils_0.0.26 sysvinit-utils_3.15-6 tar_1.35+dfsg-3.1 util-linux_2.41.3-3 xz-utils_5.8.2-2 zlib1g_1:1.3.dfsg+really1.3.1-3 zlib1g-dev_1:1.3.dfsg+really1.3.1-3 +------------------------------------------------------------------------------+ | Build Mon, 23 Feb 2026 18:16:37 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bwa-mem2 Binary: bwa-mem2 Architecture: any Version: 2.3+ds-1 Maintainer: Debian Med Packaging Team Uploaders: Dylan Aïssi , Michael R. Crusoe Homepage: https://github.com/bwa-mem2/bwa-mem2 Standards-Version: 4.7.3 Vcs-Browser: https://salsa.debian.org/med-team/bwa-mem2 Vcs-Git: https://salsa.debian.org/med-team/bwa-mem2.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, libsimde-dev, help2man Package-List: bwa-mem2 deb science optional arch=any Checksums-Sha1: 53e964d763b299ebedb1f8049d3a8082269caf37 231664 bwa-mem2_2.3+ds.orig.tar.xz 2717ababecb93207bfd08f9a64451701ef4ec4af 8300 bwa-mem2_2.3+ds-1.debian.tar.xz Checksums-Sha256: 9b864d981d626f285d04aaedd7e37eff922e611b27fabee784db7d019fe9bb89 231664 bwa-mem2_2.3+ds.orig.tar.xz 2a248b437a5385aa4ac8ba7eec70339128238ce6fdddebf7b645fc9c7f9826bb 8300 bwa-mem2_2.3+ds-1.debian.tar.xz Files: 3355c5c715a135fe6a31707b906e3944 231664 bwa-mem2_2.3+ds.orig.tar.xz 9adb0b3deec075e26f8ed2e7db3322cd 8300 bwa-mem2_2.3+ds-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmmZlV0SHGNydXNvZUBk ZWJpYW4ub3JnAAoJEDwmdj9sZ+biWDEP/jSNkBZ3Z+5Yd3kf3C9LM9snlY8iQwIB C79hjL9s9ZZZNOcb9U8OwVi1uJJny5X7yJWYykdykYPcFMI8B3rqz4uTJc9rC1Vw opWe0xpQqAWsFhjt56l2zjMtrK45aYGdd6YwYbqUD+Ep8GiJBFW1DTsI27RJdqCB XmnoNayHAtm8ar1W/OL73GjMF+Bs01gKBnv2UEsVDazbOqqTcEfYY/1G94FUY/no hK5ess0MoU+/dycCy+yrz507JRK+nZud/xaRIR86+3kUXKPrhe+yMink24UXs7+g 8dk5Sn6nFnfyqkeajCRYuttLT91nOZswiGcdErPas7+yqsDiYThHOTXEkwYdw7es 0hDpGzG/ToXsGiYmruO/uAS3y+nPAwiJup+cLLuvdbxJHrG4Elif21cKF6WIvwo2 1d1a53pTX9PTClGDv4ChqrO+Hu8jNT53sLnY/ITe0akJ7QlZN7vynw3yQtpwLu7j 5KHt8A7z9exwK+aFh/C6O3iBFROMn+mJ1LYRH9ooSMF2izi+qP9agf/hJmuv4NG8 z6n65sI4iDrOsJwigIgKVpuYcxgtuRfZnl7gz1DcdRmGbuN4OTzRG/GS+rqL8SmX EAIG5aFrwXSIEkRQrmR7RS1uFTwh2+Aw/tiuuUjJp6dYGBDSQtgTqRvD50lL0+/C pgBgGtMMMTlx =3hu0 -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./bwa-mem2_2.3+ds-1.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./bwa-mem2_2.3+ds-1.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting bwa-mem2 in /build/reproducible-path/bwa-mem2-2.3+ds dpkg-source: info: unpacking bwa-mem2_2.3+ds.orig.tar.xz dpkg-source: info: unpacking bwa-mem2_2.3+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening dpkg-source: info: applying simde dpkg-source: info: applying 0010-newer-GCC-support.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=6 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh SOURCE_DATE_EPOCH=1771672728 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -B dpkg-buildpackage: info: source package bwa-mem2 dpkg-buildpackage: info: source version 2.3+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds' dh_auto_clean || true make -j6 clean make[2]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds' rm -fr src/*.o libbwa.a bwa-mem2 bwa-mem2.sse41 bwa-mem2.sse42 bwa-mem2.avx bwa-mem2.avx2 bwa-mem2.avx512bw cd ext/safestringlib/ && make clean make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[2]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds' make[1]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds' dh_auto_build -- EXE=bwa-mem2.sse2 ARCH_FLAGS='-msse2' make -j6 INSTALL="install --strip-program=true" EXE=bwa-mem2.sse2 ARCH_FLAGS=-msse2 make[2]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make arch=sse41 EXE=bwa-mem2.sse41 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/fastmap.cpp -o src/fastmap.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwtindex.cpp -o src/bwtindex.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/utils.cpp -o src/utils.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/memcpy_bwamem.cpp -o src/memcpy_bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kthread.cpp -o src/kthread.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kstring.cpp -o src/kstring.o In file included from src/kstring.cpp:28: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/utils.cpp:44: src/utils.cpp: In function ‘pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/utils.cpp: In function ‘uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/utils.cpp: In function ‘int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)’: src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro ‘__KS_GETUNTIL’ 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro ‘KSTREAM_INIT’ 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro ‘KSEQ_INIT2’ 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/ksw.cpp -o src/ksw.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bntseq.cpp -o src/bntseq.o In file included from src/bwamem.h:47, from src/kthread.h:37, from src/kthread.cpp:32: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem.cpp -o src/bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/profiling.cpp -o src/profiling.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bandedSWA.cpp -o src/bandedSWA.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/FMI_search.cpp -o src/FMI_search.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/read_index_ele.cpp -o src/read_index_ele.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o In file included from src/bwamem.h:47, from src/fastmap.h:45, from src/fastmap.cpp:42: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o In file included from src/bwamem_pair.cpp:36: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o src/bwamem_pair.cpp: In function ‘int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)’: src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o In file included from src/bwamem.h:47, from src/bwamem.cpp:34: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:50: src/bwamem.cpp: In function ‘bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘SMEM ks_ksmall_mem_intv1(size_t, SMEM*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_chain_t ks_ksmall_mem_flt(size_t, mem_chain_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ In file included from src/bwa.cpp:39: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)’: src/bwamem.cpp:388:117: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 388 | memcpy_bwamem((char*) (auxSeedBuf), c->m * sizeof(mem_seed_t), c->seeds, c->n * sizeof(mem_seed_t), __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘SMEM* mem_collect_smem(FMI_search*, const mem_opt_t*, const bseq1_t*, int, SMEM*, int32_t*, int16_t*, uint8_t*, int32_t*, mem_cache*, int64_t&, int)’: src/bwamem.cpp:722:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 722 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem1\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:729:46: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:729:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:766:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 766 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem2\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:767:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:767:58: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp: In function ‘int mem_kernel1_core(FMI_search*, const mem_opt_t*, bseq1_t*, int, mem_chain_v*, mem_seed_t*, int64_t, mem_cache*, int)’: src/bwamem.cpp:1009:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1009 | fprintf(stderr, "[%0.4d] Re-allocating SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp: In function ‘void mem_process_seqs(mem_opt_t*, int64_t, int, bseq1_t*, const mem_pestat_t*, worker_t&)’: src/bwamem.cpp:1373:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1373 | memcpy_bwamem(pes, 4 * sizeof(mem_pestat_t), pes0, 4 * sizeof(mem_pestat_t), __FILE__, __LINE__); // if pes0 != NULL, set the insert-size | ^~~~~~~~ src/bwamem.cpp: In function ‘void* _mm_realloc(void*, int64_t, int64_t, int16_t)’: src/bwamem.cpp:1845:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1845 | memcpy_bwamem(nptr, nsize * dsize, ptr, csize, __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘void mem_chain2aln_across_reads_V2(const mem_opt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, int, mem_chain_v*, mem_alnreg_v*, mem_cache*, uint8_t*, int)’: src/bwamem.cpp:2240:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2240 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2265:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2265 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2287:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2287 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2340:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2340 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2367:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2367 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2385:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2385 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2892:60: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 2892 | "numPairsLeft: %d, numPairsRight %d, lim: %d\nExiting.\n", | ~^ | | | int | %ld 2893 | numPairsLeft, numPairsRight, *wsize_pair); | ~~~~~~~~~~~ | | | int64_t {aka long int} src/FMI_search.cpp: In member function ‘int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)’: src/FMI_search.cpp:278:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld In file included from src/bwamem.h:47, from src/bwamem_extra.cpp:33: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o src/kopen.cpp: In function ‘int ftp_open(const char*)’: src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); | ^~~~~~~~ src/kopen.cpp: In function ‘void* kopen(const char*, int*)’: src/kopen.cpp:262:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 262 | sprintf(port2, "%d", pasv_port); | ^ In file included from /usr/include/stdio.h:970, from src/kopen.cpp:30: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int ftp_open(const char*)’ at src/kopen.cpp:262:9, inlined from ‘void* kopen(const char*, int*)’ at src/kopen.cpp:325:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' mkdir -p obj mkdir -p objtest gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/abort_handler_s.o safeclib/abort_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastsame_s.o safeclib/strlastsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/ignore_handler_s.o safeclib/ignore_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpncpy_s.o safeclib/stpncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strljustify_s.o safeclib/strljustify_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp16_s.o safeclib/memcmp16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasecmp_s.o safeclib/strcasecmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncat_s.o safeclib/strncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp32_s.o safeclib/memcmp32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasestr_s.o safeclib/strcasestr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncpy_s.o safeclib/strncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp_s.o safeclib/memcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcat_s.o safeclib/strcat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnlen_s.o safeclib/strnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy16_s.o safeclib/memcpy16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmpfld_s.o safeclib/strcmpfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnterminate_s.o safeclib/strnterminate_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/main.h:36, from src/main.cpp:35: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.sse41 make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make arch=sse42 EXE=bwa-mem2.sse42 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/fastmap.cpp -o src/fastmap.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwtindex.cpp -o src/bwtindex.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/utils.cpp -o src/utils.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/memcpy_bwamem.cpp -o src/memcpy_bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kthread.cpp -o src/kthread.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kstring.cpp -o src/kstring.o In file included from src/utils.cpp:44: src/utils.cpp: In function ‘pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/utils.cpp: In function ‘uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/utils.cpp: In function ‘int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)’: src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro ‘__KS_GETUNTIL’ 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro ‘KSTREAM_INIT’ 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro ‘KSEQ_INIT2’ 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ In file included from src/kstring.cpp:28: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/ksw.cpp -o src/ksw.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bntseq.cpp -o src/bntseq.o In file included from src/bwamem.h:47, from src/kthread.h:37, from src/kthread.cpp:32: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem.cpp -o src/bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/profiling.cpp -o src/profiling.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bandedSWA.cpp -o src/bandedSWA.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/FMI_search.cpp -o src/FMI_search.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/read_index_ele.cpp -o src/read_index_ele.o In file included from src/bwamem.h:47, from src/fastmap.h:45, from src/fastmap.cpp:42: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o In file included from src/bwamem_pair.cpp:36: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o src/bwamem_pair.cpp: In function ‘int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)’: src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/bwa.cpp:39: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, from src/bwamem.cpp:34: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:50: src/bwamem.cpp: In function ‘bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘SMEM ks_ksmall_mem_intv1(size_t, SMEM*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_chain_t ks_ksmall_mem_flt(size_t, mem_chain_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ In file included from src/bwamem.h:47, from src/bwamem_extra.cpp:33: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)’: src/bwamem.cpp:388:117: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 388 | memcpy_bwamem((char*) (auxSeedBuf), c->m * sizeof(mem_seed_t), c->seeds, c->n * sizeof(mem_seed_t), __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘SMEM* mem_collect_smem(FMI_search*, const mem_opt_t*, const bseq1_t*, int, SMEM*, int32_t*, int16_t*, uint8_t*, int32_t*, mem_cache*, int64_t&, int)’: src/bwamem.cpp:722:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 722 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem1\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:729:46: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:729:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:766:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 766 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem2\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:767:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:767:58: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp: In function ‘int mem_kernel1_core(FMI_search*, const mem_opt_t*, bseq1_t*, int, mem_chain_v*, mem_seed_t*, int64_t, mem_cache*, int)’: src/bwamem.cpp:1009:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1009 | fprintf(stderr, "[%0.4d] Re-allocating SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp: In function ‘void mem_process_seqs(mem_opt_t*, int64_t, int, bseq1_t*, const mem_pestat_t*, worker_t&)’: src/bwamem.cpp:1373:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1373 | memcpy_bwamem(pes, 4 * sizeof(mem_pestat_t), pes0, 4 * sizeof(mem_pestat_t), __FILE__, __LINE__); // if pes0 != NULL, set the insert-size | ^~~~~~~~ src/bwamem.cpp: In function ‘void* _mm_realloc(void*, int64_t, int64_t, int16_t)’: src/bwamem.cpp:1845:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1845 | memcpy_bwamem(nptr, nsize * dsize, ptr, csize, __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘void mem_chain2aln_across_reads_V2(const mem_opt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, int, mem_chain_v*, mem_alnreg_v*, mem_cache*, uint8_t*, int)’: src/bwamem.cpp:2240:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2240 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2265:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2265 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2287:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2287 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2340:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2340 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2367:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2367 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2385:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2385 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2892:60: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 2892 | "numPairsLeft: %d, numPairsRight %d, lim: %d\nExiting.\n", | ~^ | | | int | %ld 2893 | numPairsLeft, numPairsRight, *wsize_pair); | ~~~~~~~~~~~ | | | int64_t {aka long int} g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Nothing to be done for 'directories'. gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/abort_handler_s.o safeclib/abort_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastsame_s.o safeclib/strlastsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/kopen.cpp: In function ‘int ftp_open(const char*)’: src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/ignore_handler_s.o safeclib/ignore_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpncpy_s.o safeclib/stpncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strljustify_s.o safeclib/strljustify_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/kopen.cpp: In function ‘void* kopen(const char*, int*)’: src/kopen.cpp:262:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 262 | sprintf(port2, "%d", pasv_port); | ^ In file included from /usr/include/stdio.h:970, from src/kopen.cpp:30: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int ftp_open(const char*)’ at src/kopen.cpp:262:9, inlined from ‘void* kopen(const char*, int*)’ at src/kopen.cpp:325:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ src/FMI_search.cpp: In member function ‘int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)’: src/FMI_search.cpp:278:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp16_s.o safeclib/memcmp16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasecmp_s.o safeclib/strcasecmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncat_s.o safeclib/strncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp32_s.o safeclib/memcmp32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasestr_s.o safeclib/strcasestr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncpy_s.o safeclib/strncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp_s.o safeclib/memcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcat_s.o safeclib/strcat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnlen_s.o safeclib/strnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy16_s.o safeclib/memcpy16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmpfld_s.o safeclib/strcmpfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnterminate_s.o safeclib/strnterminate_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/main.h:36, from src/main.cpp:35: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.sse42 make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make arch=avx EXE=bwa-mem2.avx CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/fastmap.cpp -o src/fastmap.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwtindex.cpp -o src/bwtindex.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/utils.cpp -o src/utils.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/memcpy_bwamem.cpp -o src/memcpy_bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kthread.cpp -o src/kthread.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kstring.cpp -o src/kstring.o In file included from src/utils.cpp:44: src/utils.cpp: In function ‘pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/utils.cpp: In function ‘uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/utils.cpp: In function ‘int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)’: src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro ‘__KS_GETUNTIL’ 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro ‘KSTREAM_INIT’ 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro ‘KSEQ_INIT2’ 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ In file included from src/kstring.cpp:28: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/ksw.cpp -o src/ksw.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bntseq.cpp -o src/bntseq.o In file included from src/bwamem.h:47, from src/kthread.h:37, from src/kthread.cpp:32: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem.cpp -o src/bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/profiling.cpp -o src/profiling.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bandedSWA.cpp -o src/bandedSWA.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/FMI_search.cpp -o src/FMI_search.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/read_index_ele.cpp -o src/read_index_ele.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o In file included from src/bwamem.h:47, from src/fastmap.h:45, from src/fastmap.cpp:42: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem_pair.cpp:36: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ src/bwamem_pair.cpp: In function ‘int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)’: src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/bwamem.h:47, from src/bwamem.cpp:34: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o In file included from src/bwamem.h:50: src/bwamem.cpp: In function ‘bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘SMEM ks_ksmall_mem_intv1(size_t, SMEM*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_chain_t ks_ksmall_mem_flt(size_t, mem_chain_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)’: src/bwamem.cpp:388:117: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 388 | memcpy_bwamem((char*) (auxSeedBuf), c->m * sizeof(mem_seed_t), c->seeds, c->n * sizeof(mem_seed_t), __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘SMEM* mem_collect_smem(FMI_search*, const mem_opt_t*, const bseq1_t*, int, SMEM*, int32_t*, int16_t*, uint8_t*, int32_t*, mem_cache*, int64_t&, int)’: src/bwamem.cpp:722:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 722 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem1\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:729:46: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:729:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:766:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 766 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem2\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:767:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:767:58: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp: In function ‘int mem_kernel1_core(FMI_search*, const mem_opt_t*, bseq1_t*, int, mem_chain_v*, mem_seed_t*, int64_t, mem_cache*, int)’: src/bwamem.cpp:1009:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1009 | fprintf(stderr, "[%0.4d] Re-allocating SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp: In function ‘void mem_process_seqs(mem_opt_t*, int64_t, int, bseq1_t*, const mem_pestat_t*, worker_t&)’: src/bwamem.cpp:1373:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1373 | memcpy_bwamem(pes, 4 * sizeof(mem_pestat_t), pes0, 4 * sizeof(mem_pestat_t), __FILE__, __LINE__); // if pes0 != NULL, set the insert-size | ^~~~~~~~ src/bwamem.cpp: In function ‘void* _mm_realloc(void*, int64_t, int64_t, int16_t)’: src/bwamem.cpp:1845:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1845 | memcpy_bwamem(nptr, nsize * dsize, ptr, csize, __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘void mem_chain2aln_across_reads_V2(const mem_opt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, int, mem_chain_v*, mem_alnreg_v*, mem_cache*, uint8_t*, int)’: src/bwamem.cpp:2240:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2240 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2265:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2265 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2287:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2287 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2340:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2340 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2367:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2367 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2385:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2385 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2892:60: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 2892 | "numPairsLeft: %d, numPairsRight %d, lim: %d\nExiting.\n", | ~^ | | | int | %ld 2893 | numPairsLeft, numPairsRight, *wsize_pair); | ~~~~~~~~~~~ | | | int64_t {aka long int} g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o In file included from src/bwa.cpp:39: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ src/FMI_search.cpp: In member function ‘int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)’: src/FMI_search.cpp:278:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o src/kopen.cpp: In function ‘int ftp_open(const char*)’: src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); | ^~~~~~~~ cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Nothing to be done for 'directories'. gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/abort_handler_s.o safeclib/abort_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/bwamem.h:47, from src/bwamem_extra.cpp:33: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/kopen.cpp: In function ‘void* kopen(const char*, int*)’: src/kopen.cpp:262:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 262 | sprintf(port2, "%d", pasv_port); | ^ In file included from /usr/include/stdio.h:970, from src/kopen.cpp:30: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int ftp_open(const char*)’ at src/kopen.cpp:262:9, inlined from ‘void* kopen(const char*, int*)’ at src/kopen.cpp:325:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastsame_s.o safeclib/strlastsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/ignore_handler_s.o safeclib/ignore_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpncpy_s.o safeclib/stpncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strljustify_s.o safeclib/strljustify_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp16_s.o safeclib/memcmp16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasecmp_s.o safeclib/strcasecmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncat_s.o safeclib/strncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp32_s.o safeclib/memcmp32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasestr_s.o safeclib/strcasestr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncpy_s.o safeclib/strncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp_s.o safeclib/memcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcat_s.o safeclib/strcat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnlen_s.o safeclib/strnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy16_s.o safeclib/memcpy16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmpfld_s.o safeclib/strcmpfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnterminate_s.o safeclib/strnterminate_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/main.h:36, from src/main.cpp:35: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.avx make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make arch=avx2 EXE=bwa-mem2.avx2 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/fastmap.cpp -o src/fastmap.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwtindex.cpp -o src/bwtindex.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/utils.cpp -o src/utils.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/memcpy_bwamem.cpp -o src/memcpy_bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kthread.cpp -o src/kthread.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kstring.cpp -o src/kstring.o In file included from src/utils.cpp:44: src/utils.cpp: In function ‘pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/utils.cpp: In function ‘uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/utils.cpp: In function ‘int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)’: src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro ‘__KS_GETUNTIL’ 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro ‘KSTREAM_INIT’ 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro ‘KSEQ_INIT2’ 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ In file included from src/kstring.cpp:28: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/ksw.cpp -o src/ksw.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bntseq.cpp -o src/bntseq.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem.cpp -o src/bwamem.o In file included from src/bwamem.h:47, from src/kthread.h:37, from src/kthread.cpp:32: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/profiling.cpp -o src/profiling.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bandedSWA.cpp -o src/bandedSWA.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/FMI_search.cpp -o src/FMI_search.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/read_index_ele.cpp -o src/read_index_ele.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o In file included from src/bwamem.h:47, from src/fastmap.h:45, from src/fastmap.cpp:42: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o In file included from src/bwamem_pair.cpp:36: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, from src/bwamem.cpp:34: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o In file included from src/bwamem.h:50: src/bwamem.cpp: In function ‘bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘SMEM ks_ksmall_mem_intv1(size_t, SMEM*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_chain_t ks_ksmall_mem_flt(size_t, mem_chain_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)’: src/bwamem.cpp:388:117: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 388 | memcpy_bwamem((char*) (auxSeedBuf), c->m * sizeof(mem_seed_t), c->seeds, c->n * sizeof(mem_seed_t), __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘SMEM* mem_collect_smem(FMI_search*, const mem_opt_t*, const bseq1_t*, int, SMEM*, int32_t*, int16_t*, uint8_t*, int32_t*, mem_cache*, int64_t&, int)’: src/bwamem.cpp:722:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 722 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem1\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:729:46: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:729:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:766:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 766 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem2\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:767:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:767:58: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp: In function ‘int mem_kernel1_core(FMI_search*, const mem_opt_t*, bseq1_t*, int, mem_chain_v*, mem_seed_t*, int64_t, mem_cache*, int)’: src/bwamem.cpp:1009:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1009 | fprintf(stderr, "[%0.4d] Re-allocating SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp: In function ‘void mem_process_seqs(mem_opt_t*, int64_t, int, bseq1_t*, const mem_pestat_t*, worker_t&)’: src/bwamem.cpp:1373:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1373 | memcpy_bwamem(pes, 4 * sizeof(mem_pestat_t), pes0, 4 * sizeof(mem_pestat_t), __FILE__, __LINE__); // if pes0 != NULL, set the insert-size | ^~~~~~~~ src/bwamem.cpp: In function ‘void* _mm_realloc(void*, int64_t, int64_t, int16_t)’: src/bwamem.cpp:1845:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1845 | memcpy_bwamem(nptr, nsize * dsize, ptr, csize, __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘void mem_chain2aln_across_reads_V2(const mem_opt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, int, mem_chain_v*, mem_alnreg_v*, mem_cache*, uint8_t*, int)’: src/bwamem.cpp:2240:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2240 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2265:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2265 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2287:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2287 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2340:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2340 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2367:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2367 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2385:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2385 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2892:60: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 2892 | "numPairsLeft: %d, numPairsRight %d, lim: %d\nExiting.\n", | ~^ | | | int | %ld 2893 | numPairsLeft, numPairsRight, *wsize_pair); | ~~~~~~~~~~~ | | | int64_t {aka long int} src/bwamem_pair.cpp: In function ‘int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)’: src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/bwa.cpp:39: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o src/FMI_search.cpp: In member function ‘int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)’: src/FMI_search.cpp:278:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld In file included from src/bwamem.h:47, from src/bwamem_extra.cpp:33: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o src/kopen.cpp: In function ‘int ftp_open(const char*)’: src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); | ^~~~~~~~ src/kopen.cpp: In function ‘void* kopen(const char*, int*)’: src/kopen.cpp:262:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 262 | sprintf(port2, "%d", pasv_port); | ^ In file included from /usr/include/stdio.h:970, from src/kopen.cpp:30: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int ftp_open(const char*)’ at src/kopen.cpp:262:9, inlined from ‘void* kopen(const char*, int*)’ at src/kopen.cpp:325:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Nothing to be done for 'directories'. gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/abort_handler_s.o safeclib/abort_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastsame_s.o safeclib/strlastsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/ignore_handler_s.o safeclib/ignore_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpncpy_s.o safeclib/stpncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strljustify_s.o safeclib/strljustify_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp16_s.o safeclib/memcmp16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasecmp_s.o safeclib/strcasecmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncat_s.o safeclib/strncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp32_s.o safeclib/memcmp32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasestr_s.o safeclib/strcasestr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncpy_s.o safeclib/strncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp_s.o safeclib/memcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcat_s.o safeclib/strcat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnlen_s.o safeclib/strnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy16_s.o safeclib/memcpy16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmpfld_s.o safeclib/strcmpfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnterminate_s.o safeclib/strnterminate_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/main.h:36, from src/main.cpp:35: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.avx2 make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make arch=avx512 EXE=bwa-mem2.avx512bw CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/fastmap.cpp -o src/fastmap.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwtindex.cpp -o src/bwtindex.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/utils.cpp -o src/utils.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/memcpy_bwamem.cpp -o src/memcpy_bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kthread.cpp -o src/kthread.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kstring.cpp -o src/kstring.o In file included from src/utils.cpp:44: src/utils.cpp: In function ‘pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/utils.cpp: In function ‘uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/utils.cpp: In function ‘int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)’: src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro ‘__KS_GETUNTIL’ 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro ‘KSTREAM_INIT’ 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro ‘KSEQ_INIT2’ 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ In file included from src/kstring.cpp:28: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/ksw.cpp -o src/ksw.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bntseq.cpp -o src/bntseq.o In file included from src/bwamem.h:47, from src/kthread.h:37, from src/kthread.cpp:32: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem.cpp -o src/bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/profiling.cpp -o src/profiling.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bandedSWA.cpp -o src/bandedSWA.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/FMI_search.cpp -o src/FMI_search.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/read_index_ele.cpp -o src/read_index_ele.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o In file included from src/bwamem.h:47, from src/fastmap.h:45, from src/fastmap.cpp:42: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem_pair.cpp:36: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o src/bwamem_pair.cpp: In function ‘int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)’: src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/bwa.cpp:39: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, from src/bwamem.cpp:34: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o In file included from src/bwamem.h:50: src/bwamem.cpp: In function ‘bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘SMEM ks_ksmall_mem_intv1(size_t, SMEM*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_chain_t ks_ksmall_mem_flt(size_t, mem_chain_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)’: src/bwamem.cpp:388:117: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 388 | memcpy_bwamem((char*) (auxSeedBuf), c->m * sizeof(mem_seed_t), c->seeds, c->n * sizeof(mem_seed_t), __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘SMEM* mem_collect_smem(FMI_search*, const mem_opt_t*, const bseq1_t*, int, SMEM*, int32_t*, int16_t*, uint8_t*, int32_t*, mem_cache*, int64_t&, int)’: src/bwamem.cpp:722:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 722 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem1\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:729:46: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:729:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:766:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 766 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem2\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:767:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:767:58: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp: In function ‘int mem_kernel1_core(FMI_search*, const mem_opt_t*, bseq1_t*, int, mem_chain_v*, mem_seed_t*, int64_t, mem_cache*, int)’: src/bwamem.cpp:1009:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1009 | fprintf(stderr, "[%0.4d] Re-allocating SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp: In function ‘void mem_process_seqs(mem_opt_t*, int64_t, int, bseq1_t*, const mem_pestat_t*, worker_t&)’: src/bwamem.cpp:1373:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1373 | memcpy_bwamem(pes, 4 * sizeof(mem_pestat_t), pes0, 4 * sizeof(mem_pestat_t), __FILE__, __LINE__); // if pes0 != NULL, set the insert-size | ^~~~~~~~ src/bwamem.cpp: In function ‘void* _mm_realloc(void*, int64_t, int64_t, int16_t)’: src/bwamem.cpp:1845:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1845 | memcpy_bwamem(nptr, nsize * dsize, ptr, csize, __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘void mem_chain2aln_across_reads_V2(const mem_opt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, int, mem_chain_v*, mem_alnreg_v*, mem_cache*, uint8_t*, int)’: src/bwamem.cpp:2240:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2240 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2265:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2265 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2287:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2287 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2340:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2340 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2367:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2367 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2385:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2385 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2892:60: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 2892 | "numPairsLeft: %d, numPairsRight %d, lim: %d\nExiting.\n", | ~^ | | | int | %ld 2893 | numPairsLeft, numPairsRight, *wsize_pair); | ~~~~~~~~~~~ | | | int64_t {aka long int} src/kopen.cpp: In function ‘int ftp_open(const char*)’: src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); | ^~~~~~~~ src/FMI_search.cpp: In member function ‘int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)’: src/FMI_search.cpp:278:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/kopen.cpp: In function ‘void* kopen(const char*, int*)’: src/kopen.cpp:262:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 262 | sprintf(port2, "%d", pasv_port); | ^ In file included from /usr/include/stdio.h:970, from src/kopen.cpp:30: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int ftp_open(const char*)’ at src/kopen.cpp:262:9, inlined from ‘void* kopen(const char*, int*)’ at src/kopen.cpp:325:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Nothing to be done for 'directories'. gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/abort_handler_s.o safeclib/abort_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o In file included from src/bwamem.h:47, from src/bwamem_extra.cpp:33: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastsame_s.o safeclib/strlastsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/ignore_handler_s.o safeclib/ignore_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpncpy_s.o safeclib/stpncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strljustify_s.o safeclib/strljustify_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp16_s.o safeclib/memcmp16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasecmp_s.o safeclib/strcasecmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncat_s.o safeclib/strncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp32_s.o safeclib/memcmp32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasestr_s.o safeclib/strcasestr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncpy_s.o safeclib/strncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp_s.o safeclib/memcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcat_s.o safeclib/strcat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnlen_s.o safeclib/strnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy16_s.o safeclib/memcpy16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmpfld_s.o safeclib/strcmpfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnterminate_s.o safeclib/strnterminate_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/main.h:36, from src/main.cpp:35: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.avx512bw make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -Wall -O3 src/runsimd.cpp -Iext/safestringlib/include -Lext/safestringlib/ -lsafestring -o bwa-mem2 make[2]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds' dh_auto_build -- multi make -j6 INSTALL="install --strip-program=true" multi make[2]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make arch=sse41 EXE=bwa-mem2.sse41 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/fastmap.cpp -o src/fastmap.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwtindex.cpp -o src/bwtindex.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/utils.cpp -o src/utils.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/memcpy_bwamem.cpp -o src/memcpy_bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kthread.cpp -o src/kthread.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kstring.cpp -o src/kstring.o In file included from src/utils.cpp:44: src/utils.cpp: In function ‘pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/utils.cpp: In function ‘uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/ksw.cpp -o src/ksw.o src/utils.cpp: In function ‘int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)’: src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro ‘__KS_GETUNTIL’ 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro ‘KSTREAM_INIT’ 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro ‘KSEQ_INIT2’ 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ In file included from src/kstring.cpp:28: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bntseq.cpp -o src/bntseq.o In file included from src/bwamem.h:47, from src/kthread.h:37, from src/kthread.cpp:32: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem.cpp -o src/bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/profiling.cpp -o src/profiling.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bandedSWA.cpp -o src/bandedSWA.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/FMI_search.cpp -o src/FMI_search.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/read_index_ele.cpp -o src/read_index_ele.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o In file included from src/bwamem.h:47, from src/fastmap.h:45, from src/fastmap.cpp:42: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o In file included from src/bwamem.h:47, from src/bwamem.cpp:34: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:50: src/bwamem.cpp: In function ‘bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘SMEM ks_ksmall_mem_intv1(size_t, SMEM*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_chain_t ks_ksmall_mem_flt(size_t, mem_chain_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)’: src/bwamem.cpp:388:117: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 388 | memcpy_bwamem((char*) (auxSeedBuf), c->m * sizeof(mem_seed_t), c->seeds, c->n * sizeof(mem_seed_t), __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘SMEM* mem_collect_smem(FMI_search*, const mem_opt_t*, const bseq1_t*, int, SMEM*, int32_t*, int16_t*, uint8_t*, int32_t*, mem_cache*, int64_t&, int)’: src/bwamem.cpp:722:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 722 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem1\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:729:46: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:729:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:766:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 766 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem2\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:767:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:767:58: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp: In function ‘int mem_kernel1_core(FMI_search*, const mem_opt_t*, bseq1_t*, int, mem_chain_v*, mem_seed_t*, int64_t, mem_cache*, int)’: src/bwamem.cpp:1009:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1009 | fprintf(stderr, "[%0.4d] Re-allocating SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp: In function ‘void mem_process_seqs(mem_opt_t*, int64_t, int, bseq1_t*, const mem_pestat_t*, worker_t&)’: src/bwamem.cpp:1373:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1373 | memcpy_bwamem(pes, 4 * sizeof(mem_pestat_t), pes0, 4 * sizeof(mem_pestat_t), __FILE__, __LINE__); // if pes0 != NULL, set the insert-size | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o src/bwamem.cpp: In function ‘void* _mm_realloc(void*, int64_t, int64_t, int16_t)’: src/bwamem.cpp:1845:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1845 | memcpy_bwamem(nptr, nsize * dsize, ptr, csize, __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘void mem_chain2aln_across_reads_V2(const mem_opt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, int, mem_chain_v*, mem_alnreg_v*, mem_cache*, uint8_t*, int)’: src/bwamem.cpp:2240:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2240 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2265:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2265 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2287:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2287 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2340:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2340 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2367:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2367 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2385:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2385 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2892:60: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 2892 | "numPairsLeft: %d, numPairsRight %d, lim: %d\nExiting.\n", | ~^ | | | int | %ld 2893 | numPairsLeft, numPairsRight, *wsize_pair); | ~~~~~~~~~~~ | | | int64_t {aka long int} In file included from src/bwamem_pair.cpp:36: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o src/bwamem_pair.cpp: In function ‘int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)’: src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/bwa.cpp:39: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o src/FMI_search.cpp: In member function ‘int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)’: src/FMI_search.cpp:278:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/kopen.cpp: In function ‘int ftp_open(const char*)’: src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, from src/bwamem_extra.cpp:33: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ src/kopen.cpp: In function ‘void* kopen(const char*, int*)’: src/kopen.cpp:262:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 262 | sprintf(port2, "%d", pasv_port); | ^ In file included from /usr/include/stdio.h:970, from src/kopen.cpp:30: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int ftp_open(const char*)’ at src/kopen.cpp:262:9, inlined from ‘void* kopen(const char*, int*)’ at src/kopen.cpp:325:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Nothing to be done for 'directories'. gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/abort_handler_s.o safeclib/abort_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastsame_s.o safeclib/strlastsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/ignore_handler_s.o safeclib/ignore_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpncpy_s.o safeclib/stpncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strljustify_s.o safeclib/strljustify_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp16_s.o safeclib/memcmp16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasecmp_s.o safeclib/strcasecmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncat_s.o safeclib/strncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp32_s.o safeclib/memcmp32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasestr_s.o safeclib/strcasestr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncpy_s.o safeclib/strncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp_s.o safeclib/memcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcat_s.o safeclib/strcat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnlen_s.o safeclib/strnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy16_s.o safeclib/memcpy16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmpfld_s.o safeclib/strcmpfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnterminate_s.o safeclib/strnterminate_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/main.h:36, from src/main.cpp:35: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.sse41 make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make arch=sse42 EXE=bwa-mem2.sse42 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/fastmap.cpp -o src/fastmap.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwtindex.cpp -o src/bwtindex.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/utils.cpp -o src/utils.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/memcpy_bwamem.cpp -o src/memcpy_bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kthread.cpp -o src/kthread.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kstring.cpp -o src/kstring.o In file included from src/utils.cpp:44: src/utils.cpp: In function ‘pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/utils.cpp: In function ‘uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/ksw.cpp -o src/ksw.o src/utils.cpp: In function ‘int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)’: src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro ‘__KS_GETUNTIL’ 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro ‘KSTREAM_INIT’ 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro ‘KSEQ_INIT2’ 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ In file included from src/kstring.cpp:28: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bntseq.cpp -o src/bntseq.o In file included from src/bwamem.h:47, from src/kthread.h:37, from src/kthread.cpp:32: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem.cpp -o src/bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/profiling.cpp -o src/profiling.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bandedSWA.cpp -o src/bandedSWA.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/FMI_search.cpp -o src/FMI_search.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/read_index_ele.cpp -o src/read_index_ele.o In file included from src/bwamem.h:47, from src/fastmap.h:45, from src/fastmap.cpp:42: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o In file included from src/bwa.cpp:39: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem_pair.cpp:36: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, from src/bwamem.cpp:34: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ src/bwamem_pair.cpp: In function ‘int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)’: src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from src/bwamem.h:50: src/bwamem.cpp: In function ‘bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘SMEM ks_ksmall_mem_intv1(size_t, SMEM*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_chain_t ks_ksmall_mem_flt(size_t, mem_chain_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)’: src/bwamem.cpp:388:117: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 388 | memcpy_bwamem((char*) (auxSeedBuf), c->m * sizeof(mem_seed_t), c->seeds, c->n * sizeof(mem_seed_t), __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, from src/bwamem_extra.cpp:33: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘SMEM* mem_collect_smem(FMI_search*, const mem_opt_t*, const bseq1_t*, int, SMEM*, int32_t*, int16_t*, uint8_t*, int32_t*, mem_cache*, int64_t&, int)’: src/bwamem.cpp:722:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 722 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem1\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:729:46: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:729:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:766:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 766 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem2\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:767:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:767:58: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp: In function ‘int mem_kernel1_core(FMI_search*, const mem_opt_t*, bseq1_t*, int, mem_chain_v*, mem_seed_t*, int64_t, mem_cache*, int)’: src/bwamem.cpp:1009:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1009 | fprintf(stderr, "[%0.4d] Re-allocating SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp: In function ‘void mem_process_seqs(mem_opt_t*, int64_t, int, bseq1_t*, const mem_pestat_t*, worker_t&)’: src/bwamem.cpp:1373:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1373 | memcpy_bwamem(pes, 4 * sizeof(mem_pestat_t), pes0, 4 * sizeof(mem_pestat_t), __FILE__, __LINE__); // if pes0 != NULL, set the insert-size | ^~~~~~~~ src/bwamem.cpp: In function ‘void* _mm_realloc(void*, int64_t, int64_t, int16_t)’: src/bwamem.cpp:1845:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1845 | memcpy_bwamem(nptr, nsize * dsize, ptr, csize, __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘void mem_chain2aln_across_reads_V2(const mem_opt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, int, mem_chain_v*, mem_alnreg_v*, mem_cache*, uint8_t*, int)’: src/bwamem.cpp:2240:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2240 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2265:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2265 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2287:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2287 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2340:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2340 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2367:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2367 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2385:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2385 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2892:60: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 2892 | "numPairsLeft: %d, numPairsRight %d, lim: %d\nExiting.\n", | ~^ | | | int | %ld 2893 | numPairsLeft, numPairsRight, *wsize_pair); | ~~~~~~~~~~~ | | | int64_t {aka long int} g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o src/kopen.cpp: In function ‘int ftp_open(const char*)’: src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); | ^~~~~~~~ src/FMI_search.cpp: In member function ‘int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)’: src/FMI_search.cpp:278:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Nothing to be done for 'directories'. gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/abort_handler_s.o safeclib/abort_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/kopen.cpp: In function ‘void* kopen(const char*, int*)’: src/kopen.cpp:262:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 262 | sprintf(port2, "%d", pasv_port); | ^ In file included from /usr/include/stdio.h:970, from src/kopen.cpp:30: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int ftp_open(const char*)’ at src/kopen.cpp:262:9, inlined from ‘void* kopen(const char*, int*)’ at src/kopen.cpp:325:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastsame_s.o safeclib/strlastsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/ignore_handler_s.o safeclib/ignore_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpncpy_s.o safeclib/stpncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strljustify_s.o safeclib/strljustify_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp16_s.o safeclib/memcmp16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasecmp_s.o safeclib/strcasecmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncat_s.o safeclib/strncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp32_s.o safeclib/memcmp32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasestr_s.o safeclib/strcasestr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncpy_s.o safeclib/strncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp_s.o safeclib/memcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcat_s.o safeclib/strcat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnlen_s.o safeclib/strnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy16_s.o safeclib/memcpy16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmpfld_s.o safeclib/strcmpfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnterminate_s.o safeclib/strnterminate_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/main.h:36, from src/main.cpp:35: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.sse42 make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make arch=avx EXE=bwa-mem2.avx CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/fastmap.cpp -o src/fastmap.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwtindex.cpp -o src/bwtindex.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/utils.cpp -o src/utils.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/memcpy_bwamem.cpp -o src/memcpy_bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kthread.cpp -o src/kthread.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kstring.cpp -o src/kstring.o In file included from src/utils.cpp:44: src/utils.cpp: In function ‘pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/utils.cpp: In function ‘uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/utils.cpp: In function ‘int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)’: src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro ‘__KS_GETUNTIL’ 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro ‘KSTREAM_INIT’ 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro ‘KSEQ_INIT2’ 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ In file included from src/kstring.cpp:28: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/ksw.cpp -o src/ksw.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bntseq.cpp -o src/bntseq.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem.cpp -o src/bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/profiling.cpp -o src/profiling.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bandedSWA.cpp -o src/bandedSWA.o In file included from src/bwamem.h:47, from src/kthread.h:37, from src/kthread.cpp:32: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/FMI_search.cpp -o src/FMI_search.o In file included from src/bwamem.h:47, from src/fastmap.h:45, from src/fastmap.cpp:42: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/read_index_ele.cpp -o src/read_index_ele.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o In file included from src/bwamem.h:47, from src/bwamem.cpp:34: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:50: src/bwamem.cpp: In function ‘bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘SMEM ks_ksmall_mem_intv1(size_t, SMEM*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_chain_t ks_ksmall_mem_flt(size_t, mem_chain_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)’: src/bwamem.cpp:388:117: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 388 | memcpy_bwamem((char*) (auxSeedBuf), c->m * sizeof(mem_seed_t), c->seeds, c->n * sizeof(mem_seed_t), __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘SMEM* mem_collect_smem(FMI_search*, const mem_opt_t*, const bseq1_t*, int, SMEM*, int32_t*, int16_t*, uint8_t*, int32_t*, mem_cache*, int64_t&, int)’: src/bwamem.cpp:722:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 722 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem1\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:729:46: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:729:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:766:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 766 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem2\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:767:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:767:58: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp: In function ‘int mem_kernel1_core(FMI_search*, const mem_opt_t*, bseq1_t*, int, mem_chain_v*, mem_seed_t*, int64_t, mem_cache*, int)’: src/bwamem.cpp:1009:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1009 | fprintf(stderr, "[%0.4d] Re-allocating SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp: In function ‘void mem_process_seqs(mem_opt_t*, int64_t, int, bseq1_t*, const mem_pestat_t*, worker_t&)’: src/bwamem.cpp:1373:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1373 | memcpy_bwamem(pes, 4 * sizeof(mem_pestat_t), pes0, 4 * sizeof(mem_pestat_t), __FILE__, __LINE__); // if pes0 != NULL, set the insert-size | ^~~~~~~~ src/bwamem.cpp: In function ‘void* _mm_realloc(void*, int64_t, int64_t, int16_t)’: src/bwamem.cpp:1845:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1845 | memcpy_bwamem(nptr, nsize * dsize, ptr, csize, __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘void mem_chain2aln_across_reads_V2(const mem_opt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, int, mem_chain_v*, mem_alnreg_v*, mem_cache*, uint8_t*, int)’: src/bwamem.cpp:2240:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2240 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2265:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2265 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2287:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2287 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2340:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2340 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2367:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2367 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2385:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2385 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2892:60: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 2892 | "numPairsLeft: %d, numPairsRight %d, lim: %d\nExiting.\n", | ~^ | | | int | %ld 2893 | numPairsLeft, numPairsRight, *wsize_pair); | ~~~~~~~~~~~ | | | int64_t {aka long int} g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o In file included from src/bwamem_pair.cpp:36: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ src/FMI_search.cpp: In member function ‘int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)’: src/FMI_search.cpp:278:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem_pair.cpp: In function ‘int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)’: src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o In file included from src/bwa.cpp:39: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o src/kopen.cpp: In function ‘int ftp_open(const char*)’: src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); | ^~~~~~~~ src/kopen.cpp: In function ‘void* kopen(const char*, int*)’: src/kopen.cpp:262:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 262 | sprintf(port2, "%d", pasv_port); | ^ In file included from /usr/include/stdio.h:970, from src/kopen.cpp:30: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int ftp_open(const char*)’ at src/kopen.cpp:262:9, inlined from ‘void* kopen(const char*, int*)’ at src/kopen.cpp:325:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Nothing to be done for 'directories'. gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/abort_handler_s.o safeclib/abort_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastsame_s.o safeclib/strlastsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/ignore_handler_s.o safeclib/ignore_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpncpy_s.o safeclib/stpncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strljustify_s.o safeclib/strljustify_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp16_s.o safeclib/memcmp16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasecmp_s.o safeclib/strcasecmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncat_s.o safeclib/strncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp32_s.o safeclib/memcmp32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasestr_s.o safeclib/strcasestr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncpy_s.o safeclib/strncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp_s.o safeclib/memcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcat_s.o safeclib/strcat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnlen_s.o safeclib/strnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy16_s.o safeclib/memcpy16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmpfld_s.o safeclib/strcmpfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnterminate_s.o safeclib/strnterminate_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/bwamem.h:47, from src/bwamem_extra.cpp:33: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/main.h:36, from src/main.cpp:35: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.avx make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make arch=avx2 EXE=bwa-mem2.avx2 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/fastmap.cpp -o src/fastmap.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwtindex.cpp -o src/bwtindex.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/utils.cpp -o src/utils.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/memcpy_bwamem.cpp -o src/memcpy_bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kthread.cpp -o src/kthread.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kstring.cpp -o src/kstring.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/ksw.cpp -o src/ksw.o In file included from src/kstring.cpp:28: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/utils.cpp:44: src/utils.cpp: In function ‘pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/utils.cpp: In function ‘uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/utils.cpp: In function ‘int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)’: src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro ‘__KS_GETUNTIL’ 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro ‘KSTREAM_INIT’ 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro ‘KSEQ_INIT2’ 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bntseq.cpp -o src/bntseq.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem.cpp -o src/bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/profiling.cpp -o src/profiling.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bandedSWA.cpp -o src/bandedSWA.o In file included from src/bwamem.h:47, from src/kthread.h:37, from src/kthread.cpp:32: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, from src/fastmap.h:45, from src/fastmap.cpp:42: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/FMI_search.cpp -o src/FMI_search.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/read_index_ele.cpp -o src/read_index_ele.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o In file included from src/bwamem.h:47, from src/bwamem.cpp:34: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:50: src/bwamem.cpp: In function ‘bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘SMEM ks_ksmall_mem_intv1(size_t, SMEM*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_chain_t ks_ksmall_mem_flt(size_t, mem_chain_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)’: src/bwamem.cpp:388:117: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 388 | memcpy_bwamem((char*) (auxSeedBuf), c->m * sizeof(mem_seed_t), c->seeds, c->n * sizeof(mem_seed_t), __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘SMEM* mem_collect_smem(FMI_search*, const mem_opt_t*, const bseq1_t*, int, SMEM*, int32_t*, int16_t*, uint8_t*, int32_t*, mem_cache*, int64_t&, int)’: src/bwamem.cpp:722:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 722 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem1\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:729:46: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:729:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:766:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 766 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem2\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:767:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:767:58: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp: In function ‘int mem_kernel1_core(FMI_search*, const mem_opt_t*, bseq1_t*, int, mem_chain_v*, mem_seed_t*, int64_t, mem_cache*, int)’: src/bwamem.cpp:1009:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1009 | fprintf(stderr, "[%0.4d] Re-allocating SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp: In function ‘void mem_process_seqs(mem_opt_t*, int64_t, int, bseq1_t*, const mem_pestat_t*, worker_t&)’: src/bwamem.cpp:1373:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1373 | memcpy_bwamem(pes, 4 * sizeof(mem_pestat_t), pes0, 4 * sizeof(mem_pestat_t), __FILE__, __LINE__); // if pes0 != NULL, set the insert-size | ^~~~~~~~ src/bwamem.cpp: In function ‘void* _mm_realloc(void*, int64_t, int64_t, int16_t)’: src/bwamem.cpp:1845:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1845 | memcpy_bwamem(nptr, nsize * dsize, ptr, csize, __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘void mem_chain2aln_across_reads_V2(const mem_opt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, int, mem_chain_v*, mem_alnreg_v*, mem_cache*, uint8_t*, int)’: src/bwamem.cpp:2240:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2240 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2265:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2265 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2287:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2287 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2340:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2340 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2367:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2367 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2385:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2385 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2892:60: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 2892 | "numPairsLeft: %d, numPairsRight %d, lim: %d\nExiting.\n", | ~^ | | | int | %ld 2893 | numPairsLeft, numPairsRight, *wsize_pair); | ~~~~~~~~~~~ | | | int64_t {aka long int} In file included from src/bwamem_pair.cpp:36: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwa.cpp:39: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ src/FMI_search.cpp: In member function ‘int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)’: src/FMI_search.cpp:278:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o src/bwamem_pair.cpp: In function ‘int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)’: src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o src/kopen.cpp: In function ‘int ftp_open(const char*)’: src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); | ^~~~~~~~ cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Nothing to be done for 'directories'. gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/abort_handler_s.o safeclib/abort_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS src/kopen.cpp: In function ‘void* kopen(const char*, int*)’: src/kopen.cpp:262:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 262 | sprintf(port2, "%d", pasv_port); | ^ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from /usr/include/stdio.h:970, from src/kopen.cpp:30: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int ftp_open(const char*)’ at src/kopen.cpp:262:9, inlined from ‘void* kopen(const char*, int*)’ at src/kopen.cpp:325:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastsame_s.o safeclib/strlastsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/ignore_handler_s.o safeclib/ignore_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpncpy_s.o safeclib/stpncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strljustify_s.o safeclib/strljustify_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp16_s.o safeclib/memcmp16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasecmp_s.o safeclib/strcasecmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncat_s.o safeclib/strncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp32_s.o safeclib/memcmp32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasestr_s.o safeclib/strcasestr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncpy_s.o safeclib/strncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/bwamem.h:47, from src/bwamem_extra.cpp:33: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp_s.o safeclib/memcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcat_s.o safeclib/strcat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnlen_s.o safeclib/strnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy16_s.o safeclib/memcpy16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmpfld_s.o safeclib/strcmpfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnterminate_s.o safeclib/strnterminate_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/main.h:36, from src/main.cpp:35: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.avx2 make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make arch=avx512 EXE=bwa-mem2.avx512bw CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/fastmap.cpp -o src/fastmap.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwtindex.cpp -o src/bwtindex.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/utils.cpp -o src/utils.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/memcpy_bwamem.cpp -o src/memcpy_bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kthread.cpp -o src/kthread.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kstring.cpp -o src/kstring.o In file included from src/utils.cpp:44: src/utils.cpp: In function ‘pair64_t ks_ksmall_128(size_t, pair64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:46:1: note: in expansion of macro ‘KSORT_INIT’ 46 | KSORT_INIT(128, pair64_t, pair64_lt) | ^~~~~~~~~~ src/utils.cpp: In function ‘uint64_t ks_ksmall_64(size_t, uint64_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/utils.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(64, uint64_t, ks_lt_generic) | ^~~~~~~~~~ src/utils.cpp: In function ‘int ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)’: src/kseq.h:135:109: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 135 | memcpy_bwamem(str->s + str->l, str->m - str->l, ks->buf + ks->begin, i - ks->begin, __FILE__, __LINE__); \ | ^~~~~~~~ src/kseq.h:159:9: note: in expansion of macro ‘__KS_GETUNTIL’ 159 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ src/kseq.h:237:9: note: in expansion of macro ‘KSTREAM_INIT’ 237 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ src/utils.cpp:50:1: note: in expansion of macro ‘KSEQ_INIT2’ 50 | KSEQ_INIT2(, gzFile, err_gzread) | ^~~~~~~~~~ In file included from src/kstring.cpp:28: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/ksw.cpp -o src/ksw.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bntseq.cpp -o src/bntseq.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem.cpp -o src/bwamem.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/profiling.cpp -o src/profiling.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bandedSWA.cpp -o src/bandedSWA.o In file included from src/bwamem.h:47, from src/kthread.h:37, from src/kthread.cpp:32: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/FMI_search.cpp -o src/FMI_search.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/read_index_ele.cpp -o src/read_index_ele.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_pair.cpp -o src/bwamem_pair.o In file included from src/bwamem.h:47, from src/fastmap.h:45, from src/fastmap.cpp:42: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:47, from src/bwamem.cpp:34: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ In file included from src/bwamem.h:50: src/bwamem.cpp: In function ‘bwtintv_t ks_ksmall_mem_intv(size_t, bwtintv_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:47:1: note: in expansion of macro ‘KSORT_INIT’ 47 | KSORT_INIT(mem_intv, bwtintv_t, intv_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘SMEM ks_ksmall_mem_intv1(size_t, SMEM*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:49:1: note: in expansion of macro ‘KSORT_INIT’ 49 | KSORT_INIT(mem_intv1, SMEM, intv_lt1) // debug | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_chain_t ks_ksmall_mem_flt(size_t, mem_chain_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:65:1: note: in expansion of macro ‘KSORT_INIT’ 65 | KSORT_INIT(mem_flt, mem_chain_t, flt_lt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:153:1: note: in expansion of macro ‘KSORT_INIT’ 153 | KSORT_INIT(mem_ars2, mem_alnreg_t, alnreg_slt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:156:1: note: in expansion of macro ‘KSORT_INIT’ 156 | KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:159:1: note: in expansion of macro ‘KSORT_INIT’ 159 | KSORT_INIT(mem_ars_hash, mem_alnreg_t, alnreg_hlt) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘mem_alnreg_t ks_ksmall_mem_ars_hash2(size_t, mem_alnreg_t*, size_t)’: src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:246:61: note: in expansion of macro ‘KSORT_SWAP’ 246 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:250:53: note: in expansion of macro ‘KSORT_SWAP’ 250 | if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:251:53: note: in expansion of macro ‘KSORT_SWAP’ 251 | if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:252:52: note: in expansion of macro ‘KSORT_SWAP’ 252 | if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:253:25: note: in expansion of macro ‘KSORT_SWAP’ 253 | KSORT_SWAP(type_t, *mid, *(low+1)); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:259:33: note: in expansion of macro ‘KSORT_SWAP’ 259 | KSORT_SWAP(type_t, *ll, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 78 | #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } | ^ src/ksort.h:261:25: note: in expansion of macro ‘KSORT_SWAP’ 261 | KSORT_SWAP(type_t, *low, *hh); \ | ^~~~~~~~~~ src/bwamem.cpp:162:1: note: in expansion of macro ‘KSORT_INIT’ 162 | KSORT_INIT(mem_ars_hash2, mem_alnreg_t, alnreg_hlt2) | ^~~~~~~~~~ src/bwamem.cpp: In function ‘int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int, int)’: src/bwamem.cpp:388:117: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 388 | memcpy_bwamem((char*) (auxSeedBuf), c->m * sizeof(mem_seed_t), c->seeds, c->n * sizeof(mem_seed_t), __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘SMEM* mem_collect_smem(FMI_search*, const mem_opt_t*, const bseq1_t*, int, SMEM*, int32_t*, int16_t*, uint8_t*, int32_t*, mem_cache*, int64_t&, int)’: src/bwamem.cpp:722:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 722 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem1\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:729:46: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:729:53: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 729 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:766:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 766 | fprintf(stderr, "[%0.4d] REA Re-allocating SMEM data structures after num_smem2\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:767:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:767:58: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 767 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp: In function ‘int mem_kernel1_core(FMI_search*, const mem_opt_t*, bseq1_t*, int, mem_chain_v*, mem_seed_t*, int64_t, mem_cache*, int)’: src/bwamem.cpp:1009:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1009 | fprintf(stderr, "[%0.4d] Re-allocating SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp: In function ‘void mem_process_seqs(mem_opt_t*, int64_t, int, bseq1_t*, const mem_pestat_t*, worker_t&)’: src/bwamem.cpp:1373:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1373 | memcpy_bwamem(pes, 4 * sizeof(mem_pestat_t), pes0, 4 * sizeof(mem_pestat_t), __FILE__, __LINE__); // if pes0 != NULL, set the insert-size | ^~~~~~~~ src/bwamem.cpp: In function ‘void* _mm_realloc(void*, int64_t, int64_t, int16_t)’: src/bwamem.cpp:1845:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1845 | memcpy_bwamem(nptr, nsize * dsize, ptr, csize, __FILE__, __LINE__); | ^~~~~~~~ src/bwamem.cpp: In function ‘void mem_chain2aln_across_reads_V2(const mem_opt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, int, mem_chain_v*, mem_alnreg_v*, mem_cache*, uint8_t*, int)’: src/bwamem.cpp:2240:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2240 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2265:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2265 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2287:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2287 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2340:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2340 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2367:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2367 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2385:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2385 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2892:60: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 2892 | "numPairsLeft: %d, numPairsRight %d, lim: %d\nExiting.\n", | ~^ | | | int | %ld 2893 | numPairsLeft, numPairsRight, *wsize_pair); | ~~~~~~~~~~~ | | | int64_t {aka long int} In file included from src/bwamem_pair.cpp:36: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ src/FMI_search.cpp: In member function ‘int FMI_search::build_fm_index(const char*, char*, int64_t, int64_t*, int64_t*)’: src/FMI_search.cpp:278:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 278 | fprintf(stderr, "pos: %d, ref_seq_len__: %ld\n", pos, ref_seq_len >> SA_COMPX); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem_pair.cpp: In function ‘int mem_matesw_batch_pre(const mem_opt_t*, const bntseq_t*, const uint8_t*, const mem_pestat_t*, const mem_alnreg_t*, int, const uint8_t*, mem_alnreg_v*, mem_cache*, int, int32_t, int32_t&, int32_t&, int32_t)’: src/bwamem_pair.cpp:1028:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1028 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufRefs in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1045:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1045 | fprintf(stderr, "[0000][%0.4d] Re-allocating (doubling) seqBufQers in %s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem_pair.cpp:1062:33: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1062 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairs in %s\n", tid, __func__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kswv.cpp -o src/kswv.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwa.cpp -o src/bwa.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/bwamem_extra.cpp -o src/bwamem_extra.o In file included from src/bwa.cpp:39: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/kopen.cpp -o src/kopen.o src/kopen.cpp: In function ‘int ftp_open(const char*)’: src/kopen.cpp:257:69: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 257 | memcpy_bwamem(pasv_ip, 4 * sizeof(int), v, 4 * sizeof(int), __FILE__, __LINE__); | ^~~~~~~~ src/kopen.cpp: In function ‘void* kopen(const char*, int*)’: src/kopen.cpp:262:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 262 | sprintf(port2, "%d", pasv_port); | ^ In file included from /usr/include/stdio.h:970, from src/kopen.cpp:30: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int ftp_open(const char*)’ at src/kopen.cpp:262:9, inlined from ‘void* kopen(const char*, int*)’ at src/kopen.cpp:325:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' make[4]: Nothing to be done for 'directories'. gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/abort_handler_s.o safeclib/abort_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastsame_s.o safeclib/strlastsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/ignore_handler_s.o safeclib/ignore_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Isrc -Iext/safestringlib/include src/main.cpp -o src/main.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/stpncpy_s.o safeclib/stpncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strljustify_s.o safeclib/strljustify_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp16_s.o safeclib/memcmp16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/bwamem.h:47, from src/bwamem_extra.cpp:33: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasecmp_s.o safeclib/strcasecmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncat_s.o safeclib/strncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp32_s.o safeclib/memcmp32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcasestr_s.o safeclib/strcasestr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strncpy_s.o safeclib/strncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcmp_s.o safeclib/memcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcat_s.o safeclib/strcat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnlen_s.o safeclib/strnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy16_s.o safeclib/memcpy16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmpfld_s.o safeclib/strcmpfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strnterminate_s.o safeclib/strnterminate_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy32_s.o safeclib/memcpy32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcmp_s.o safeclib/strcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memcpy_s.o safeclib/memcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldin_s.o safeclib/strcpyfldin_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strprefix_s.o safeclib/strprefix_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfldout_s.o safeclib/strcpyfldout_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS In file included from src/main.h:36, from src/main.cpp:35: src/kstring.h: In function ‘int kputsn(const char*, int, kstring_t*)’: src/kstring.h:69:55: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 69 | memcpy_bwamem(s->s + s->l, s->m - s->l, p, l, __FILE__, __LINE__); | ^~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds/ext/safestringlib' ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/kopen.o g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -mavx512bw -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now src/main.o libbwa.a -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -o bwa-mem2.avx512bw make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O3 -fpermissive -msse -msse2 -msse3 -mssse3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -Wl,-z,relro -Wl,-z,now -Wall -O3 src/runsimd.cpp -Iext/safestringlib/include -Lext/safestringlib/ -lsafestring -o bwa-mem2 make[2]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds' help2man --no-discard-stderr --version-string="2.3+ds" \ --help-option=' ' --no-info ./bwa-mem2 --name="Sequence alignment using Burrows-Wheeler Transform" \ > debian/bwa-mem2.1 help2man --no-discard-stderr --version-string="2.3+ds" \ --help-option=' ' --no-info './bwa-mem2 mem' \ --include <(echo -e "[NAME]\nbwa-mem2_mem \- Sequence alignment using Burrows-Wheeler Transform") \ > debian/bwa-mem2-mem.1 make[1]: Leaving directory '/build/reproducible-path/bwa-mem2-2.3+ds' dh_auto_test -a create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/bwa-mem2/ -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'bwa-mem2' in '../bwa-mem2_2.3+ds-1_amd64.deb'. dpkg-deb: building package 'bwa-mem2-dbgsym' in '../bwa-mem2-dbgsym_2.3+ds-1_amd64.deb'. dpkg-genbuildinfo --build=any -O../bwa-mem2_2.3+ds-1_amd64.buildinfo dpkg-genchanges --build=any -O../bwa-mem2_2.3+ds-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2026-02-23T18:18:04Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 23 Feb 2026 18:18:05 +0000 | +------------------------------------------------------------------------------+ bwa-mem2_2.3+ds-1_amd64.changes: -------------------------------- Format: 1.8 Date: Sat, 21 Feb 2026 12:18:48 +0100 Source: bwa-mem2 Binary: bwa-mem2 bwa-mem2-dbgsym Architecture: amd64 Version: 2.3+ds-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: bwa-mem2 - Sequence alignment using Burrows-Wheeler Transform Changes: bwa-mem2 (2.3+ds-1) unstable; urgency=medium . * d/watch: upgrade to uscan 5 syntax * New upstream version * Standards-Version: 4.7.3 (routine-update) * debputy lint --auto-fix (routine-update) * Removed many patches that were applied upstream. * Add +ds suffix, as we removed the ".git" directory from the upstream tarball. * d/clean: enable repeat builds Checksums-Sha1: e29dac3d975a9e49c192ee75072ca9a1eb3fc75f 2028784 bwa-mem2-dbgsym_2.3+ds-1_amd64.deb e59b031fcb9139cc0bf46ed37a2b7a7970114b29 4895 bwa-mem2_2.3+ds-1_amd64.buildinfo f04ce26faec2917bea048ffdf782a988ef08e98b 376580 bwa-mem2_2.3+ds-1_amd64.deb Checksums-Sha256: 6671ab2a5f74fa7965949f1cff86bc3ce2b13a9fb7bfb1f8860a3f92c46857eb 2028784 bwa-mem2-dbgsym_2.3+ds-1_amd64.deb 7057e59f801c07e797c433ec1364f8bc6f5912727f744cbd4840f8280fd0433c 4895 bwa-mem2_2.3+ds-1_amd64.buildinfo d42304114cec1ef5d74881ee38682b66c06f96b2edac27757f7c51273769224b 376580 bwa-mem2_2.3+ds-1_amd64.deb Files: d7411e639e060426cb815e56646f5c8b 2028784 debug optional bwa-mem2-dbgsym_2.3+ds-1_amd64.deb 4cac46e900c1b522a75e430cc1f13c53 4895 science optional bwa-mem2_2.3+ds-1_amd64.buildinfo f524e381a6ebc0da50e101d5544d04e5 376580 science optional bwa-mem2_2.3+ds-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Mon, 23 Feb 2026 18:18:05 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: bwa-mem2 Binary: bwa-mem2 bwa-mem2-dbgsym Architecture: amd64 Version: 2.3+ds-1 Checksums-Md5: d7411e639e060426cb815e56646f5c8b 2028784 bwa-mem2-dbgsym_2.3+ds-1_amd64.deb f524e381a6ebc0da50e101d5544d04e5 376580 bwa-mem2_2.3+ds-1_amd64.deb Checksums-Sha1: e29dac3d975a9e49c192ee75072ca9a1eb3fc75f 2028784 bwa-mem2-dbgsym_2.3+ds-1_amd64.deb f04ce26faec2917bea048ffdf782a988ef08e98b 376580 bwa-mem2_2.3+ds-1_amd64.deb Checksums-Sha256: 6671ab2a5f74fa7965949f1cff86bc3ce2b13a9fb7bfb1f8860a3f92c46857eb 2028784 bwa-mem2-dbgsym_2.3+ds-1_amd64.deb d42304114cec1ef5d74881ee38682b66c06f96b2edac27757f7c51273769224b 376580 bwa-mem2_2.3+ds-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 23 Feb 2026 18:18:04 +0000 Build-Path: /build/reproducible-path/bwa-mem2-2.3+ds Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.18.1-3), autopoint (= 0.23.2-1), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.8), bash (= 5.3-2), binutils (= 2.46-2), binutils-common (= 2.46-2), binutils-x86-64-linux-gnu (= 2.46-2), bsdextrautils (= 2.41.3-3), build-essential (= 12.12), bzip2 (= 1.0.8-6+b1), coreutils (= 9.7-3), cpp (= 4:15.2.0-5), cpp-15 (= 15.2.0-13), cpp-15-x86-64-linux-gnu (= 15.2.0-13), cpp-x86-64-linux-gnu (= 4:15.2.0-5), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 13.30), debianutils (= 5.23.2), dh-autoreconf (= 21+nmu1), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), dpkg (= 1.23.5), dpkg-dev (= 1.23.5), dwz (= 0.16-2), file (= 1:5.46-5+b1), findutils (= 4.10.0-3), g++ (= 4:15.2.0-5), g++-15 (= 15.2.0-13), g++-15-x86-64-linux-gnu (= 15.2.0-13), g++-x86-64-linux-gnu (= 4:15.2.0-5), gcc (= 4:15.2.0-5), gcc-15 (= 15.2.0-13), gcc-15-base (= 15.2.0-13), gcc-15-x86-64-linux-gnu (= 15.2.0-13), gcc-x86-64-linux-gnu (= 4:15.2.0-5), gettext (= 0.23.2-1), gettext-base (= 0.23.2-1), grep (= 3.12-1), groff-base (= 1.23.0-10), gzip (= 1.13-1), help2man (= 1.49.3), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-13), libatomic1 (= 15.2.0-13), libattr1 (= 1:2.5.2-4), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46-2), libblkid1 (= 2.41.3-3), libbz2-1.0 (= 1.0.8-6+b1), libc-bin (= 2.42-13), libc-dev-bin (= 2.42-13), libc-gconv-modules-extra (= 2.42-13), libc6 (= 2.42-13), libc6-dev (= 2.42-13), libcap-ng0 (= 0.8.5-4+b2), libcap2 (= 1:2.75-10+b5), libcc1-0 (= 15.2.0-13), libcrypt1 (= 1:4.5.1-1), libctf-nobfd0 (= 2.46-2), libctf0 (= 2.46-2), libdb5.3t64 (= 5.3.28+dfsg2-11), libdebconfclient0 (= 0.282+b2), libdebhelper-perl (= 13.30), libdpkg-perl (= 1.23.5), libelf1t64 (= 0.194-1), libfile-stripnondeterminism-perl (= 1.15.0-1), libgcc-15-dev (= 15.2.0-13), libgcc-s1 (= 15.2.0-13), libgdbm-compat4t64 (= 1.26-1+b1), libgdbm6t64 (= 1.26-1+b1), libgmp10 (= 2:6.3.0+dfsg-5+b1), libgomp1 (= 15.2.0-13), libgprofng0 (= 2.46-2), libhwasan0 (= 15.2.0-13), libisl23 (= 0.27-1+b1), libitm1 (= 15.2.0-13), libjansson4 (= 2.14-2+b4), liblocale-gettext-perl (= 1.07-8), liblsan0 (= 15.2.0-13), liblzma5 (= 5.8.2-2), libmagic-mgc (= 1:5.46-5+b1), libmagic1t64 (= 1:5.46-5+b1), libmd0 (= 1.1.0-2+b2), libmount1 (= 2.41.3-3), libmpc3 (= 1.3.1-2+b1), libmpfr6 (= 4.2.2-2+b1), libpam-modules (= 1.7.0-5+b1), libpam-modules-bin (= 1.7.0-5+b1), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5+b1), libpcre2-8-0 (= 10.46-1+b1), libperl5.40 (= 5.40.1-7), libpipeline1 (= 1.5.8-2), libquadmath0 (= 15.2.0-13), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.9-4+b1), libsframe3 (= 2.46-2), libsimde-dev (= 0.8.2-3), libsmartcols1 (= 2.41.3-3), libssl3t64 (= 3.5.5-1), libstdc++-15-dev (= 15.2.0-13), libstdc++6 (= 15.2.0-13), libsystemd0 (= 259.1-1), libtinfo6 (= 6.6+20251231-1), libtool (= 2.5.4-9), libtsan2 (= 15.2.0-13), libubsan1 (= 15.2.0-13), libuchardet0 (= 0.0.8-2+b1), libudev1 (= 259.1-1), libunistring5 (= 1.3-2+b1), libuuid1 (= 2.41.3-3), libxml2-16 (= 2.15.1+dfsg-2+b1), libzstd1 (= 1.5.7+dfsg-3+b1), linux-libc-dev (= 6.18.12-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260129-1), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1), openssl-provider-legacy (= 3.5.5-1), patch (= 2.8-2), perl (= 5.40.1-7), perl-base (= 5.40.1-7), perl-modules-5.40 (= 5.40.1-7), po-debconf (= 1.0.22), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.26), sysvinit-utils (= 3.15-6), tar (= 1.35+dfsg-3.1), util-linux (= 2.41.3-3), xz-utils (= 5.8.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-3) Environment: DEB_BUILD_OPTIONS="parallel=6" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1771672728" +------------------------------------------------------------------------------+ | Package contents Mon, 23 Feb 2026 18:18:06 +0000 | +------------------------------------------------------------------------------+ bwa-mem2-dbgsym_2.3+ds-1_amd64.deb ---------------------------------- new Debian package, version 2.0. size 2028784 bytes: control archive=852 bytes. 582 bytes, 12 lines control 721 bytes, 7 lines md5sums Package: bwa-mem2-dbgsym Source: bwa-mem2 Version: 2.3+ds-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2439 Depends: bwa-mem2 (= 2.3+ds-1) Section: debug Priority: optional Description: debug symbols for bwa-mem2 Build-Ids: 0f38b3dd41661fbe8c4214af2e052550f0401324 2cc4aa02c4195121233697234567be6127bc42d3 3c9f6d703b4eddba726e8a6f6b00a704656240ec 6960b5187aaa0445a3dc4a726793ce000541eb35 96e61ed284b77c7a905461c691e9fdbe725126da c2ed82adf90986f17c9cc62fdaddbc13d9813fa5 drwxr-xr-x root/root 0 2026-02-21 11:18 ./ drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/ drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/lib/ drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/lib/debug/.build-id/0f/ -rw-r--r-- root/root 469552 2026-02-21 11:18 ./usr/lib/debug/.build-id/0f/38b3dd41661fbe8c4214af2e052550f0401324.debug drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/lib/debug/.build-id/2c/ -rw-r--r-- root/root 467576 2026-02-21 11:18 ./usr/lib/debug/.build-id/2c/c4aa02c4195121233697234567be6127bc42d3.debug drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/lib/debug/.build-id/3c/ -rw-r--r-- root/root 467200 2026-02-21 11:18 ./usr/lib/debug/.build-id/3c/9f6d703b4eddba726e8a6f6b00a704656240ec.debug drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/lib/debug/.build-id/69/ -rw-r--r-- root/root 470992 2026-02-21 11:18 ./usr/lib/debug/.build-id/69/60b5187aaa0445a3dc4a726793ce000541eb35.debug drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/lib/debug/.build-id/96/ -rw-r--r-- root/root 496936 2026-02-21 11:18 ./usr/lib/debug/.build-id/96/e61ed284b77c7a905461c691e9fdbe725126da.debug drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/lib/debug/.build-id/c2/ -rw-r--r-- root/root 21328 2026-02-21 11:18 ./usr/lib/debug/.build-id/c2/ed82adf90986f17c9cc62fdaddbc13d9813fa5.debug drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 83616 2026-02-21 11:18 ./usr/lib/debug/.dwz/x86_64-linux-gnu/bwa-mem2.debug drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/share/ drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-02-21 11:18 ./usr/share/doc/bwa-mem2-dbgsym -> bwa-mem2 bwa-mem2_2.3+ds-1_amd64.deb --------------------------- new Debian package, version 2.0. size 376580 bytes: control archive=1336 bytes. 1028 bytes, 20 lines control 1054 bytes, 16 lines md5sums Package: bwa-mem2 Version: 2.3+ds-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1747 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.4), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: https://github.com/bwa-mem2/bwa-mem2 Description: Sequence alignment using Burrows-Wheeler Transform BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads. drwxr-xr-x root/root 0 2026-02-21 11:18 ./ drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/ drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/bin/ -rwxr-xr-x root/root 18664 2026-02-21 11:18 ./usr/bin/bwa-mem2 -rwxr-xr-x root/root 334488 2026-02-21 11:18 ./usr/bin/bwa-mem2.avx -rwxr-xr-x root/root 346776 2026-02-21 11:18 ./usr/bin/bwa-mem2.avx2 -rwxr-xr-x root/root 371352 2026-02-21 11:18 ./usr/bin/bwa-mem2.avx512bw -rwxr-xr-x root/root 342680 2026-02-21 11:18 ./usr/bin/bwa-mem2.sse41 -rwxr-xr-x root/root 342680 2026-02-21 11:18 ./usr/bin/bwa-mem2.sse42 drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/share/ drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/share/doc/bwa-mem2/ -rw-r--r-- root/root 1435 2025-06-30 07:45 ./usr/share/doc/bwa-mem2/NEWS.md.gz -rw-r--r-- root/root 3233 2025-06-30 07:45 ./usr/share/doc/bwa-mem2/README.md.gz -rw-r--r-- root/root 384 2026-02-21 11:18 ./usr/share/doc/bwa-mem2/changelog.Debian.gz -rw-r--r-- root/root 4573 2026-02-21 11:18 ./usr/share/doc/bwa-mem2/copyright drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/share/doc/bwa-mem2/examples/ -rw-r--r-- root/root 96 2024-04-16 08:41 ./usr/share/doc/bwa-mem2/examples/read1.fq -rw-r--r-- root/root 96 2024-04-16 08:41 ./usr/share/doc/bwa-mem2/examples/read2.fq -rw-r--r-- root/root 384 2024-04-16 08:41 ./usr/share/doc/bwa-mem2/examples/reads.fq -rw-r--r-- root/root 192 2024-04-16 08:41 ./usr/share/doc/bwa-mem2/examples/ref.fa drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/share/man/ drwxr-xr-x root/root 0 2026-02-21 11:18 ./usr/share/man/man1/ -rw-r--r-- root/root 1658 2026-02-21 11:18 ./usr/share/man/man1/bwa-mem2-mem.1.gz -rw-r--r-- root/root 366 2026-02-21 11:18 ./usr/share/man/man1/bwa-mem2.1.gz +------------------------------------------------------------------------------+ | Post Build Mon, 23 Feb 2026 18:18:06 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 23 Feb 2026 18:18:06 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 23 Feb 2026 18:18:07 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 25068 Build-Time: 86 Distribution: unstable Host Architecture: amd64 Install-Time: 2 Job: /srv/rebuilderd/tmp/rebuilderdkZTweZ/inputs/bwa-mem2_2.3+ds-1.dsc Machine Architecture: amd64 Package: bwa-mem2 Package-Time: 95 Source-Version: 2.3+ds-1 Space: 25068 Status: successful Version: 2.3+ds-1 -------------------------------------------------------------------------------- Finished at 2026-02-23T18:18:04Z Build needed 00:01:35, 25068k disk space size differs for bwa-mem2_2.3+ds-1_amd64.deb build artifacts stored in /srv/rebuilderd/tmp/rebuilderdkZTweZ/out checking bwa-mem2-dbgsym_2.3+ds-1_amd64.deb: size... sha256... md5... sha1... all OK checking bwa-mem2_2.3+ds-1_amd64.deb: