=============================================================================== 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/rebuilderdS6PC0H/inputs/bwa-mem2_2.2.1-1+b1_amd64.buildinfo Source: bwa-mem2 Version: 2.2.1-1 rebuilderd-worker node: osuosl4-amd64 +------------------------------------------------------------------------------+ | Downloading sources Tue, 02 Sep 2025 19:25:44 +0000 | +------------------------------------------------------------------------------+ Get:1 https://deb.debian.org/debian trixie InRelease [138 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 [47.1 kB] Get:4 https://deb.debian.org/debian trixie-proposed-updates InRelease [58.9 kB] Get:5 https://deb.debian.org/debian trixie-backports InRelease [53.7 kB] Get:6 https://deb.debian.org/debian forky InRelease [146 kB] Get:7 https://deb.debian.org/debian sid InRelease [216 kB] Get:8 https://deb.debian.org/debian experimental InRelease [101 kB] Get:9 https://deb.debian.org/debian trixie/non-free-firmware Sources [6,536 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 [38.4 kB] Get:12 https://deb.debian.org/debian trixie-updates/main Sources [54.1 kB] Get:13 https://deb.debian.org/debian trixie-proposed-updates/main Sources [108 kB] Get:14 https://deb.debian.org/debian trixie-backports/main Sources [18.9 kB] Get:15 https://deb.debian.org/debian forky/non-free-firmware Sources [7,132 B] Get:16 https://deb.debian.org/debian forky/main Sources [10.7 MB] Get:17 https://deb.debian.org/debian sid/main Sources [11.1 MB] Get:18 https://deb.debian.org/debian sid/non-free-firmware Sources [9,104 B] Get:19 https://deb.debian.org/debian experimental/non-free-firmware Sources [2,572 B] Get:20 https://deb.debian.org/debian experimental/main Sources [490 kB] Fetched 33.8 MB in 4s (8,527 kB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/b/bwa-mem2/bwa-mem2_2.2.1-1.dsc' bwa-mem2_2.2.1-1.dsc 2014 SHA256:2253cac5f88618aae3360be49a87aee1f1df1d871af2c05cca03223a102a3d05 'https://deb.debian.org/debian/pool/main/b/bwa-mem2/bwa-mem2_2.2.1.orig.tar.xz' bwa-mem2_2.2.1.orig.tar.xz 230828 SHA256:75c67d795f79fd3a3a42dd655aec3e6aee3ac231d46a5ae7214e2448df0ce450 'https://deb.debian.org/debian/pool/main/b/bwa-mem2/bwa-mem2_2.2.1-1.debian.tar.xz' bwa-mem2_2.2.1-1.debian.tar.xz 26796 SHA256:ba3e5b966151d9d1af0ab13a45949420f350d422e872eb6ccb0050fc1b167816 75c67d795f79fd3a3a42dd655aec3e6aee3ac231d46a5ae7214e2448df0ce450 bwa-mem2_2.2.1.orig.tar.xz ba3e5b966151d9d1af0ab13a45949420f350d422e872eb6ccb0050fc1b167816 bwa-mem2_2.2.1-1.debian.tar.xz 2253cac5f88618aae3360be49a87aee1f1df1d871af2c05cca03223a102a3d05 bwa-mem2_2.2.1-1.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Tue, 02 Sep 2025 19:25:48 +0000 | +------------------------------------------------------------------------------+ Rebuilding bwa-mem2=2.2.1-1 in /srv/rebuilderd/tmp/rebuilderdS6PC0H/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdS6PC0H/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdS6PC0H/inputs/bwa-mem2_2.2.1-1+b1_amd64.buildinfo /srv/rebuilderd/tmp/rebuilderdS6PC0H/inputs/bwa-mem2_2.2.1-1+b1_amd64.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/bwa-mem2-2.2.1 I: verifying dsc... successful! Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie InRelease [175 kB] Get:2 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 Packages [9684 kB] Fetched 9859 kB in 1s (9113 kB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20250430T203420Z/dists/trixie/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 openssl-provider-legacy amd64 3.5.0-1 [307 kB] Fetched 307 kB in 0s (17.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbc2wkk62/openssl-provider-legacy_3.5.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libaudit1 amd64 1:4.0.2-2+b2 [55.1 kB] Fetched 55.1 kB in 0s (5232 kB/s) dpkg-name: info: moved 'libaudit1_1%3a4.0.2-2+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmpv8ias9pt/libaudit1_4.0.2-2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libmpc3 amd64 1.3.1-1+b3 [52.2 kB] Fetched 52.2 kB in 0s (5184 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl75599qs/libmpc3_1.3.1-1+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 gzip amd64 1.13-1 [138 kB] Fetched 138 kB in 0s (13.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppdmxirdd/gzip_1.13-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libctf0 amd64 2.44-3 [88.6 kB] Fetched 88.6 kB in 0s (8795 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp26anxoyn/libctf0_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libgmp10 amd64 2:6.3.0+dfsg-3 [560 kB] Fetched 560 kB in 0s (43.7 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-3_amd64.deb' to '/srv/rebuilderd/tmp/tmp7db1nj0p/libgmp10_6.3.0+dfsg-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 liblzma5 amd64 5.8.1-1 [309 kB] Fetched 309 kB in 0s (28.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuhpyg1tx/liblzma5_5.8.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libsystemd0 amd64 257.5-2 [453 kB] Fetched 453 kB in 0s (35.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzdwy2raa/libsystemd0_257.5-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libblkid1 amd64 2.41-4 [171 kB] Fetched 171 kB in 0s (17.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2tfcrxyi/libblkid1_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 help2man amd64 1.49.3 [198 kB] Fetched 198 kB in 0s (17.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4tu17f07/help2man_1.49.3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 ncurses-base all 6.5+20250216-2 [273 kB] Fetched 273 kB in 0s (22.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph8zkduyr/ncurses-base_6.5+20250216-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 hostname amd64 3.25 [11.0 kB] Fetched 11.0 kB in 0s (1036 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp953aw4q3/hostname_3.25_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libisl23 amd64 0.27-1 [659 kB] Fetched 659 kB in 0s (48.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1dbt740b/libisl23_0.27-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 build-essential amd64 12.12 [4624 B] Fetched 4624 B in 0s (451 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu1uky0s8/build-essential_12.12_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libstdc++-14-dev amd64 14.2.0-19 [2376 kB] Fetched 2376 kB in 0s (94.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptmhp_66h/libstdc++-14-dev_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 tar amd64 1.35+dfsg-3.1 [815 kB] Fetched 815 kB in 0s (52.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpextopd2k/tar_1.35+dfsg-3.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Fetched 243 kB in 0s (20.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu36n58um/gettext-base_0.23.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 binutils-common amd64 2.44-3 [2509 kB] Fetched 2509 kB in 0s (103 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjq8kt30y/binutils-common_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-19 [12.1 MB] Fetched 12.1 MB in 0s (135 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf1_gput6/g++-14-x86-64-linux-gnu_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libgcc-s1 amd64 14.2.0-19 [72.8 kB] Fetched 72.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmr5zyb22/libgcc-s1_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Fetched 477 kB in 0s (39.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2q4v7nwc/libunistring5_1.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Fetched 770 kB in 0s (48.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe_k8n7jm/autopoint_0.23.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libmount1 amd64 2.41-4 [209 kB] Fetched 209 kB in 0s (18.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpui37z2rv/libmount1_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libseccomp2 amd64 2.6.0-2 [51.7 kB] Fetched 51.7 kB in 0s (5088 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_l42fnjl/libseccomp2_2.6.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Fetched 19.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpod1m1lns/libfile-stripnondeterminism-perl_1.14.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Fetched 248 kB in 0s (23.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx7_jtd6j/po-debconf_1.0.21+nmu1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 bash amd64 5.2.37-2 [1500 kB] Fetched 1500 kB in 0s (79.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2pnvtha9/bash_5.2.37-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libperl5.40 amd64 5.40.1-3 [4320 kB] Fetched 4320 kB in 0s (112 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprpv_0udr/libperl5.40_5.40.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 dpkg-dev all 1.22.18 [1338 kB] Fetched 1338 kB in 0s (68.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpod7pjal8/dpkg-dev_1.22.18_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 xz-utils amd64 5.8.1-1 [660 kB] Fetched 660 kB in 0s (43.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplzbonf0g/xz-utils_5.8.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libpam-modules amd64 1.7.0-3 [177 kB] Fetched 177 kB in 0s (16.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjqpl27no/libpam-modules_1.7.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Fetched 137 kB in 0s (12.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvdsv0cxy/libgomp1_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 bsdextrautils amd64 2.41-4 [94.6 kB] Fetched 94.6 kB in 0s (7712 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp12nk_c4w/bsdextrautils_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 g++ amd64 4:14.2.0-1 [1344 B] Fetched 1344 B in 0s (0 B/s) dpkg-name: info: moved 'g++_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpsisz180d/g++_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Fetched 698 kB in 0s (46.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyo84yz4l/libxml2_2.12.7+dfsg+really2.9.14-0.4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libssl3t64 amd64 3.5.0-1 [2432 kB] Fetched 2432 kB in 0s (94.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpffkpq4ra/libssl3t64_3.5.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libzstd1 amd64 1.5.7+dfsg-1 [304 kB] Fetched 304 kB in 0s (25.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplpy1q2di/libzstd1_1.5.7+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 dpkg amd64 1.22.18 [1545 kB] Fetched 1545 kB in 0s (78.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgbwyieee/dpkg_1.22.18_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (9619 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr81xaukh/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libatomic1 amd64 14.2.0-19 [9308 B] Fetched 9308 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptj1flrax/libatomic1_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 bsdutils amd64 1:2.41-4 [110 kB] Fetched 110 kB in 0s (8354 kB/s) dpkg-name: info: moved 'bsdutils_1%3a2.41-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpo_w6zugt/bsdutils_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libmd0 amd64 1.1.0-2+b1 [36.3 kB] Fetched 36.3 kB in 0s (3249 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxqag7n2d/libmd0_1.1.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Fetched 8620 B in 0s (844 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6xbwb1ld/dh-strip-nondeterminism_1.14.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 debhelper all 13.24.2 [919 kB] Fetched 919 kB in 0s (58.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd7rc1j8g/debhelper_13.24.2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libitm1 amd64 14.2.0-19 [26.0 kB] Fetched 26.0 kB in 0s (2520 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwsadugk_/libitm1_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 g++-14 amd64 14.2.0-19 [22.5 kB] Fetched 22.5 kB in 0s (2246 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwcbc3co7/g++-14_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 make amd64 4.4.1-2 [463 kB] Fetched 463 kB in 0s (38.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpezc5r31r/make_4.4.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Fetched 494 kB in 0s (39.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf42dw9xc/autoconf_2.72-3.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 patch amd64 2.8-1 [134 kB] Fetched 134 kB in 0s (12.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprqappwfl/patch_2.8-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libgprofng0 amd64 2.44-3 [808 kB] Fetched 808 kB in 0s (48.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjm80j0dc/libgprofng0_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libtool all 2.5.4-4 [539 kB] Fetched 539 kB in 0s (38.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0q9q3tfs/libtool_2.5.4-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libdpkg-perl all 1.22.18 [649 kB] Fetched 649 kB in 0s (45.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_aq5ztet/libdpkg-perl_1.22.18_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 debianutils amd64 5.22 [92.2 kB] Fetched 92.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp418e9ldd/debianutils_5.22_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 dash amd64 0.5.12-12 [98.5 kB] Fetched 98.5 kB in 0s (9674 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2roorr07/dash_0.5.12-12_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-9 [704 kB] Fetched 704 kB in 0s (49.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbwnv2vxz/libdb5.3t64_5.3.28+dfsg2-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libsmartcols1 amd64 2.41-4 [143 kB] Fetched 143 kB in 0s (13.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg32t9ko4/libsmartcols1_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1 [1436 B] Fetched 1436 B in 0s (0 B/s) dpkg-name: info: moved 'gcc-x86-64-linux-gnu_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp07e8b2l6/gcc-x86-64-linux-gnu_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libpcre2-8-0 amd64 10.45-1 [298 kB] Fetched 298 kB in 0s (27.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpknaqfa11/libpcre2-8-0_10.45-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 m4 amd64 1.4.19-7 [294 kB] Fetched 294 kB in 0s (25.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzawxozup/m4_1.4.19-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 findutils amd64 4.10.0-3 [700 kB] Fetched 700 kB in 0s (51.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7rkpypg7/findutils_4.10.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libcc1-0 amd64 14.2.0-19 [42.8 kB] Fetched 42.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp81bymljp/libcc1-0_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libacl1 amd64 2.3.2-2+b1 [32.9 kB] Fetched 32.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4w2cwhyn/libacl1_2.3.2-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1 [4840 B] Fetched 4840 B in 0s (0 B/s) dpkg-name: info: moved 'cpp-x86-64-linux-gnu_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpdkfzwlde/cpp-x86-64-linux-gnu_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Fetched 1185 kB in 0s (65.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprt1b3mic/groff-base_1.23.0-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libpam-runtime all 1.7.0-3 [248 kB] Fetched 248 kB in 0s (20.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp45h0spwi/libpam-runtime_1.7.0-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libgcc-14-dev amd64 14.2.0-19 [2672 kB] Fetched 2672 kB in 0s (100 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxrasmuzg/libgcc-14-dev_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 ncurses-bin amd64 6.5+20250216-2 [438 kB] Fetched 438 kB in 0s (33.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnof6r6ow/ncurses-bin_6.5+20250216-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 gcc-14 amd64 14.2.0-19 [540 kB] Fetched 540 kB in 0s (44.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcz1ibjj_/gcc-14_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Fetched 467 kB in 0s (13.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpibto5jn1/libsimde-dev_0.8.2-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 920 kB in 0s (60.4 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpzkdyxiv0/zlib1g-dev_1.3.dfsg+really1.3.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-19 [21.4 MB] Fetched 21.4 MB in 0s (140 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcdf1uaju/gcc-14-x86-64-linux-gnu_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/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/tmpo5we444k/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libasan8 amd64 14.2.0-19 [2725 kB] Fetched 2725 kB in 0s (26.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwqkn6knx/libasan8_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Fetched 75.2 kB in 0s (2264 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgd0h1z8x/libgdbm6t64_1.24-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 bzip2 amd64 1.0.8-6 [40.5 kB] Fetched 40.5 kB in 0s (3889 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeyguhjhu/bzip2_1.0.8-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libcrypt1 amd64 1:4.4.38-1 [90.1 kB] Fetched 90.1 kB in 0s (8505 kB/s) dpkg-name: info: moved 'libcrypt1_1%3a4.4.38-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp8s0ho8f3/libcrypt1_4.4.38-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libbinutils amd64 2.44-3 [534 kB] Fetched 534 kB in 0s (42.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp95l09vv2/libbinutils_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 linux-libc-dev all 6.12.22-1 [2542 kB] Fetched 2542 kB in 0s (9156 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv2h60uri/linux-libc-dev_6.12.22-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Fetched 24.8 kB in 0s (2350 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0fvrp22o/sensible-utils_0.0.24_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libuuid1 amd64 2.41-4 [37.6 kB] Fetched 37.6 kB in 0s (3719 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2m_nwfn3/libuuid1_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Fetched 90.9 kB in 0s (8417 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp83e6zyy9/libdebhelper-perl_13.24.2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libjansson4 amd64 2.14-2+b3 [39.8 kB] Fetched 39.8 kB in 0s (3595 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb011gl5f/libjansson4_2.14-2+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libsframe1 amd64 2.44-3 [78.4 kB] Fetched 78.4 kB in 0s (7078 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprgj0b3p3/libsframe1_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Fetched 17.1 kB in 0s (1688 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5r3hyk_z/dh-autoreconf_20_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Fetched 60.2 kB in 0s (5679 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnxhr14j_/autotools-dev_20240727.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Fetched 68.9 kB in 0s (6365 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv0fxnuru/libuchardet0_0.0.8-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Fetched 1420 kB in 0s (69.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoldcbmnw/man-db_2.13.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 sysvinit-utils amd64 3.14-4 [34.1 kB] Fetched 34.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplorr6djh/sysvinit-utils_3.14-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libstdc++6 amd64 14.2.0-19 [714 kB] Fetched 714 kB in 0s (53.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp49xmfak2/libstdc++6_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 binutils amd64 2.44-3 [265 kB] Fetched 265 kB in 0s (23.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmsekjdp7/binutils_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 gcc-14-base amd64 14.2.0-19 [49.4 kB] Fetched 49.4 kB in 0s (4791 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0h6uvgd4/gcc-14-base_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1+b1 [88.9 kB] Fetched 88.9 kB in 0s (0 B/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp_y030rof/zlib1g_1.3.dfsg+really1.3.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libcap-ng0 amd64 0.8.5-4+b1 [17.6 kB] Fetched 17.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8lmbo7qj/libcap-ng0_0.8.5-4+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Fetched 110 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd9uk4ay4/dwz_0.15-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 init-system-helpers all 1.68 [38.7 kB] Fetched 38.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsybxc3ic/init-system-helpers_1.68_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Fetched 338 kB in 0s (29.4 MB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.46-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpvozrxztn/libmagic-mgc_5.46-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 mawk amd64 1.3.4.20250131-1 [141 kB] Fetched 141 kB in 0s (13.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu5ccaxln/mawk_1.3.4.20250131-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Fetched 189 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1430kvrl/libelf1t64_0.192-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Fetched 43.6 kB in 0s (0 B/s) dpkg-name: info: moved 'file_1%3a5.46-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp_mp7gos3/file_5.46-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libattr1 amd64 1:2.5.2-3 [22.9 kB] Fetched 22.9 kB in 0s (0 B/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpd25titpr/libattr1_2.5.2-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libdebconfclient0 amd64 0.278 [10.5 kB] Fetched 10.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphjmshaen/libdebconfclient0_0.278_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libubsan1 amd64 14.2.0-19 [1074 kB] Fetched 1074 kB in 0s (63.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpewvdb5o_/libubsan1_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libtsan2 amd64 14.2.0-19 [2460 kB] Fetched 2460 kB in 0s (90.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpksdenedq/libtsan2_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libc-bin amd64 2.41-7 [636 kB] Fetched 636 kB in 0s (49.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd909qpla/libc-bin_2.41-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 perl-base amd64 5.40.1-3 [1665 kB] Fetched 1665 kB in 0s (80.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpim_nl53p/perl-base_5.40.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libc6-dev amd64 2.41-7 [1992 kB] Fetched 1992 kB in 0s (81.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_6yarwx6/libc6-dev_2.41-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libpam0g amd64 1.7.0-3 [69.7 kB] Fetched 69.7 kB in 0s (6662 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfhdi5tyy/libpam0g_1.7.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Fetched 15.3 kB in 0s (1514 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwa77bmby/liblocale-gettext-perl_1.07-7+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 sed amd64 4.9-2 [329 kB] Fetched 329 kB in 0s (29.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2mk6ovlc/sed_4.9-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1 [1200 B] Fetched 1200 B in 0s (0 B/s) dpkg-name: info: moved 'g++-x86-64-linux-gnu_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpzqsd_lbt/g++-x86-64-linux-gnu_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Fetched 1680 kB in 0s (80.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp260cmnva/gettext_0.23.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libquadmath0 amd64 14.2.0-19 [145 kB] Fetched 145 kB in 0s (10.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdkilx97t/libquadmath0_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 base-files amd64 13.7 [73.0 kB] Fetched 73.0 kB in 0s (6413 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfip55wfx/base-files_13.7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libc-dev-bin amd64 2.41-7 [57.3 kB] Fetched 57.3 kB in 0s (4895 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5subfoz2/libc-dev-bin_2.41-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 util-linux amd64 2.41-4 [1234 kB] Fetched 1234 kB in 0s (67.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp21of2u95/util-linux_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libtinfo6 amd64 6.5+20250216-2 [348 kB] Fetched 348 kB in 0s (26.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp77a1t1xv/libtinfo6_6.5+20250216-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-19 [11.0 MB] Fetched 11.0 MB in 0s (115 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq5wqjmhq/cpp-14-x86-64-linux-gnu_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libc6 amd64 2.41-7 [2847 kB] Fetched 2847 kB in 0s (98.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1gr1nr83/libc6_2.41-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 grep amd64 3.11-4 [431 kB] Fetched 431 kB in 0s (34.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvls4vb0l/grep_3.11-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 cpp-14 amd64 14.2.0-19 [1280 B] Fetched 1280 B in 0s (126 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwqkyidmq/cpp-14_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 debconf all 1.5.91 [121 kB] Fetched 121 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfj5blfkg/debconf_1.5.91_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libselinux1 amd64 3.8.1-1 [84.7 kB] Fetched 84.7 kB in 0s (7083 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfe9zn5x3/libselinux1_3.8.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 base-passwd amd64 3.6.7 [53.7 kB] Fetched 53.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4bjbu92r/base-passwd_3.6.7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libudev1 amd64 257.5-2 [151 kB] Fetched 151 kB in 0s (14.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbc6_wll9/libudev1_257.5-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 gcc amd64 4:14.2.0-1 [5136 B] Fetched 5136 B in 0s (494 kB/s) dpkg-name: info: moved 'gcc_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpp2durtig/gcc_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libctf-nobfd0 amd64 2.44-3 [156 kB] Fetched 156 kB in 0s (15.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa8ph_z1o/libctf-nobfd0_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libsqlite3-0 amd64 3.46.1-3 [913 kB] Fetched 913 kB in 0s (58.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6pxa6ow5/libsqlite3-0_3.46.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Fetched 42.0 kB in 0s (4160 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu7eh214c/libpipeline1_1.5.8-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libaudit-common all 1:4.0.2-2 [12.7 kB] Fetched 12.7 kB in 0s (1221 kB/s) dpkg-name: info: moved 'libaudit-common_1%3a4.0.2-2_all.deb' to '/srv/rebuilderd/tmp/tmph7xptovk/libaudit-common_4.0.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 diffutils amd64 1:3.10-3 [385 kB] Fetched 385 kB in 0s (32.7 MB/s) dpkg-name: info: moved 'diffutils_1%3a3.10-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpt2cnke4i/diffutils_3.10-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libbz2-1.0 amd64 1.0.8-6 [37.9 kB] Fetched 37.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpud14c3hj/libbz2-1.0_1.0.8-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 liblsan0 amd64 14.2.0-19 [1204 kB] Fetched 1204 kB in 0s (73.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa8yz7ydm/liblsan0_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libmpfr6 amd64 4.2.2-1 [729 kB] Fetched 729 kB in 0s (51.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx_h7nyz_/libmpfr6_4.2.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 perl-modules-5.40 all 5.40.1-3 [3021 kB] Fetched 3021 kB in 0s (106 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp8mu7g40/perl-modules-5.40_5.40.1-3_all.deb' Downloading dependency 1 of 147: openssl-provider-legacy:amd64=3.5.0-1 Downloading dependency 2 of 147: libaudit1:amd64=1:4.0.2-2+b2 Downloading dependency 3 of 147: libmpc3:amd64=1.3.1-1+b3 Downloading dependency 4 of 147: gzip:amd64=1.13-1 Downloading dependency 5 of 147: libctf0:amd64=2.44-3 Downloading dependency 6 of 147: libgmp10:amd64=2:6.3.0+dfsg-3 Downloading dependency 7 of 147: liblzma5:amd64=5.8.1-1 Downloading dependency 8 of 147: libsystemd0:amd64=257.5-2 Downloading dependency 9 of 147: libblkid1:amd64=2.41-4 Downloading dependency 10 of 147: help2man:amd64=1.49.3 Downloading dependency 11 of 147: ncurses-base:amd64=6.5+20250216-2 Downloading dependency 12 of 147: hostname:amd64=3.25 Downloading dependency 13 of 147: libisl23:amd64=0.27-1 Downloading dependency 14 of 147: build-essential:amd64=12.12 Downloading dependency 15 of 147: libstdc++-14-dev:amd64=14.2.0-19 Downloading dependency 16 of 147: tar:amd64=1.35+dfsg-3.1 Downloading dependency 17 of 147: gettext-base:amd64=0.23.1-1 Downloading dependency 18 of 147: binutils-common:amd64=2.44-3 Downloading dependency 19 of 147: g++-14-x86-64-linux-gnu:amd64=14.2.0-19 Downloading dependency 20 of 147: libgcc-s1:amd64=14.2.0-19 Downloading dependency 21 of 147: libunistring5:amd64=1.3-2 Downloading dependency 22 of 147: autopoint:amd64=0.23.1-1 Downloading dependency 23 of 147: libmount1:amd64=2.41-4 Downloading dependency 24 of 147: libseccomp2:amd64=2.6.0-2 Downloading dependency 25 of 147: libfile-stripnondeterminism-perl:amd64=1.14.1-2 Downloading dependency 26 of 147: po-debconf:amd64=1.0.21+nmu1 Downloading dependency 27 of 147: bash:amd64=5.2.37-2 Downloading dependency 28 of 147: libperl5.40:amd64=5.40.1-3 Downloading dependency 29 of 147: dpkg-dev:amd64=1.22.18 Downloading dependency 30 of 147: xz-utils:amd64=5.8.1-1 Downloading dependency 31 of 147: libpam-modules:amd64=1.7.0-3 Downloading dependency 32 of 147: libgomp1:amd64=14.2.0-19 Downloading dependency 33 of 147: bsdextrautils:amd64=2.41-4 Downloading dependency 34 of 147: g++:amd64=4:14.2.0-1 Downloading dependency 35 of 147: libxml2:amd64=2.12.7+dfsg+really2.9.14-0.4 Downloading dependency 36 of 147: libssl3t64:amd64=3.5.0-1 Downloading dependency 37 of 147: libzstd1:amd64=1.5.7+dfsg-1 Downloading dependency 38 of 147: dpkg:amd64=1.22.18 Downloading dependency 39 of 147: libarchive-zip-perl:amd64=1.68-1 Downloading dependency 40 of 147: libatomic1:amd64=14.2.0-19 Downloading dependency 41 of 147: bsdutils:amd64=1:2.41-4 Downloading dependency 42 of 147: libmd0:amd64=1.1.0-2+b1 Downloading dependency 43 of 147: dh-strip-nondeterminism:amd64=1.14.1-2 Downloading dependency 44 of 147: debhelper:amd64=13.24.2 Downloading dependency 45 of 147: libitm1:amd64=14.2.0-19 Downloading dependency 46 of 147: g++-14:amd64=14.2.0-19 Downloading dependency 47 of 147: make:amd64=4.4.1-2 Downloading dependency 48 of 147: autoconf:amd64=2.72-3.1 Downloading dependency 49 of 147: patch:amd64=2.8-1 Downloading dependency 50 of 147: libgprofng0:amd64=2.44-3 Downloading dependency 51 of 147: libtool:amd64=2.5.4-4 Downloading dependency 52 of 147: libdpkg-perl:amd64=1.22.18 Downloading dependency 53 of 147: debianutils:amd64=5.22 Downloading dependency 54 of 147: dash:amd64=0.5.12-12 Downloading dependency 55 of 147: libdb5.3t64:amd64=5.3.28+dfsg2-9 Downloading dependency 56 of 147: libsmartcols1:amd64=2.41-4 Downloading dependency 57 of 147: gcc-x86-64-linux-gnu:amd64=4:14.2.0-1 Downloading dependency 58 of 147: libpcre2-8-0:amd64=10.45-1 Downloading dependency 59 of 147: m4:amd64=1.4.19-7 Downloading dependency 60 of 147: findutils:amd64=4.10.0-3 Downloading dependency 61 of 147: libcc1-0:amd64=14.2.0-19 Downloading dependency 62 of 147: libacl1:amd64=2.3.2-2+b1 Downloading dependency 63 of 147: cpp-x86-64-linux-gnu:amd64=4:14.2.0-1 Downloading dependency 64 of 147: groff-base:amd64=1.23.0-7 Downloading dependency 65 of 147: libpam-runtime:amd64=1.7.0-3 Downloading dependency 66 of 147: libgcc-14-dev:amd64=14.2.0-19 Downloading dependency 67 of 147: ncurses-bin:amd64=6.5+20250216-2 Downloading dependency 68 of 147: gcc-14:amd64=14.2.0-19 Downloading dependency 69 of 147: libsimde-dev:amd64=0.8.2-3 Downloading dependency 70 of 147: zlib1g-dev:amd64=1:1.3.dfsg+really1.3.1-1+b1 Downloading dependency 71 of 147: gcc-14-x86-64-linux-gnu:amd64=14.2.0-19 Downloading dependency 72 of 147: intltool-debian:amd64=0.35.0+20060710.6 Downloading dependency 73 of 147: libasan8:amd64=14.2.0-19 Downloading dependency 74 of 147: libgdbm6t64:amd64=1.24-2 Downloading dependency 75 of 147: bzip2:amd64=1.0.8-6 Downloading dependency 76 of 147: libcrypt1:amd64=1:4.4.38-1 Downloading dependency 77 of 147: libbinutils:amd64=2.44-3 Downloading dependency 78 of 147: linux-libc-dev:amd64=6.12.22-1 Downloading dependency 79 of 147: sensible-utils:amd64=0.0.24 Downloading dependency 80 of 147: libuuid1:amd64=2.41-4 Downloading dependency 81 of 147: libdebhelper-perl:amd64=13.24.2 Downloading dependency 82 of 147: libjansson4:amd64=2.14-2+b3 Downloading dependency 83 of 147: libsframe1:amd64=2.44-3 Downloading dependency 84 of 147: dh-autoreconf:amd64=20 Downloading dependency 85 of 147: autotools-dev:amd64=20240727.1 Downloading dependency 86 of 147: libuchardet0:amd64=0.0.8-1+b2 Downloading dependency 87 of 147: man-db:amd64=2.13.0-1 Downloading dependency 88 of 147: sysvinit-utils:amd64=3.14-4 Downloading dependency 89 of 147: libstdc++6:amd64=14.2.0-19 Downloading dependency 90 of 147: binutils:amd64=2.44-3 Downloading dependency 91 of 147: gcc-14-base:amd64=14.2.0-19 Downloading dependency 92 of 147: zlib1g:amd64=1:1.3.dfsg+really1.3.1-1+b1 Downloading dependency 93 of 147: libcap-ng0:amd64=0.8.5-4+b1 Downloading dependency 94 of 147: dwz:amd64=0.15-1+b1 Downloading dependency 95 of 147: init-system-helpers:amd64=1.68 Downloading dependency 96 of 147: libmagic-mgc:amd64=1:5.46-5 Downloading dependency 97 of 147: mawk:amd64=1.3.4.20250131-1 Downloading dependency 98 of 147: libelf1t64:amd64=0.192-4 Downloading dependency 99 of 147: file:amd64=1:5.46-5 Downloading dependency 100 of 147: libattr1:amd64=1:2.5.2-3 Downloading dependency 101 of 147: libdebconfclient0:amd64=0.278 Downloading dependency 102 of 147: libubsan1:amd64=14.2.0-19 Downloading dependency 103 of 147: libtsan2:amd64=14.2.0-19 Downloading dependency 104 of 147: libc-bin:amd64=2.41-7 Downloading dependency 105 of 147: perl-base:amd64=5.40.1-3 Downloading dependency 106 of 147: libc6-dev:amd64=2.41-7 Downloading dependency 107 of 147: libpam0g:amd64=1.7.0-3 Downloading dependency 108 of 147: liblocale-gettext-perl:amd64=1.07-7+b1 Downloading dependency 109 of 147: sed:amd64=4.9-2 Downloading dependency 110 of 147: g++-x86-64-linux-gnu:amd64=4:14.2.0-1 Downloading dependency 111 of 147: gettext:amd64=0.23.1-1 Downloading dependency 112 of 147: libquadmath0:amd64=14.2.0-19 Downloading dependency 113 of 147: base-files:amd64=13.7 Downloading dependency 114 of 147: libc-dev-bin:amd64=2.41-7 Downloading dependency 115 of 147: util-linux:amd64=2.41-4 Downloading dependency 116 of 147: libtinfo6:amd64=6.5+20250216-2 Downloading dependency 117 of 147: cpp-14-x86-64-linux-gnu:amd64=14.2.0-19 Downloading dependency 118 of 147: libc6:amd64=2.41-7 Downloading dependency 119 of 147: grep:amd64=3.11-4 Downloading dependency 120 of 147: cpp-14:amd64=14.2.0-19 Downloading dependency 121 of 147: debconf:amd64=1.5.91 Downloading dependency 122 of 147: libselinux1:amd64=3.8.1-1 Downloading dependency 123 of 147: base-passwd:amd64=3.6.7 Downloading dependency 124 of 147: libudev1:amd64=257.5-2 Downloading dependency 125 of 147: gcc:amd64=4:14.2.0-1 Downloading dependency 126 of 147: libctf-nobfd0:amd64=2.44-3 Downloading dependency 127 of 147: libsqlite3-0:amd64=3.46.1-3 Downloading dependency 128 of 147: libpipeline1:amd64=1.5.8-1 Downloading dependency 129 of 147: libaudit-common:amd64=1:4.0.2-2 Downloading dependency 130 of 147: diffutils:amd64=1:3.10-3 Downloading dependency 131 of 147: libbz2-1.0:amd64=1.0.8-6 Downloading dependency 132 of 147: liblsan0:amd64=14.2.0-19 Downloading dependency 133 of 147: libmpfr6:amd64=4.2.2-1 Downloading dependency 134 of 147: perl-modules-5.40:amd64=5.40.1-3 Downloading dependency 135 of 147: libpam-modules-bin:amd64=1.7.0-3Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libpam-modules-bin amd64 1.7.0-3 [48.9 kB] Fetched 48.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8u25sna_/libpam-modules-bin_1.7.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 liblastlog2-2 amd64 2.41-4 [28.4 kB] Fetched 28.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyi0nsb24/liblastlog2-2_2.41-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Fetched 50.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_w29rvuw/libgdbm-compat4t64_1.24-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 cpp amd64 4:14.2.0-1 [1568 B] Fetched 1568 B in 0s (0 B/s) dpkg-name: info: moved 'cpp_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp5mufyk49/cpp_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libcrypt-dev amd64 1:4.4.38-1 [119 kB] Fetched 119 kB in 0s (0 B/s) dpkg-name: info: moved 'libcrypt-dev_1%3a4.4.38-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpi94opb4m/libcrypt-dev_4.4.38-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 coreutils amd64 9.7-1 [3012 kB] Fetched 3012 kB in 0s (105 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy3bcjvu1/coreutils_9.7-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Fetched 109 kB in 0s (10.9 MB/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.46-5_amd64.deb' to '/srv/rebuilderd/tmp/tmpk1hwb837/libmagic1t64_5.46-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libhwasan0 amd64 14.2.0-19 [1488 kB] Fetched 1488 kB in 0s (83.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_ktljic2/libhwasan0_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 libcap2 amd64 1:2.75-6 [28.0 kB] Fetched 28.0 kB in 0s (1352 kB/s) dpkg-name: info: moved 'libcap2_1%3a2.75-6_amd64.deb' to '/srv/rebuilderd/tmp/tmpsb6vubti/libcap2_2.75-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3 [1014 kB] Fetched 1014 kB in 0s (69.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr9k790v9/binutils-x86-64-linux-gnu_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 perl amd64 5.40.1-3 [267 kB] Fetched 267 kB in 0s (25.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph11ur87l/perl_5.40.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/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/tmpt0g38op6/rpcsvc-proto_1.4.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250430T203420Z trixie/main amd64 automake all 1:1.17-4 [862 kB] Fetched 862 kB in 0s (60.2 MB/s) dpkg-name: info: moved 'automake_1%3a1.17-4_all.deb' to '/srv/rebuilderd/tmp/tmp3wpqh54v/automake_1.17-4_all.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/tmpd4pzpjqq/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.mE5o4mom7e as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.mE5o4mom7e 127.0.0.1 - - [02/Sep/2025 19:26:49] code 404, message File not found 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:41641 ./ InRelease 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:41641 ./ Release [462 B] 127.0.0.1 - - [02/Sep/2025 19:26:49] code 404, message File not found 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:41641 ./ Release.gpg 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:41641 ./ Packages [181 kB] Fetched 182 kB in 0s (8892 kB/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 - - [02/Sep/2025 19:26:49] "GET /./gcc-14-base_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libc6_2.41-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libgcc-s1_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./mawk_1.3.4.20250131-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./base-files_13.7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libtinfo6_6.5%2b20250216-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./debianutils_5.22_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./bash_5.2.37-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libcap2_2.75-6_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libsystemd0_257.5-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./bsdutils_2.41-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libacl1_2.3.2-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libattr1_2.5.2-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libgmp10_6.3.0%2bdfsg-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libpcre2-8-0_10.45-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libselinux1_3.8.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libzstd1_1.5.7%2bdfsg-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./zlib1g_1.3.dfsg%2breally1.3.1-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libssl3t64_3.5.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./openssl-provider-legacy_3.5.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./coreutils_9.7-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./dash_0.5.12-12_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./diffutils_3.10-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libbz2-1.0_1.0.8-6_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./liblzma5_5.8.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libmd0_1.1.0-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./tar_1.35%2bdfsg-3.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./dpkg_1.22.18_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./findutils_4.10.0-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./grep_3.11-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./gzip_1.13-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./hostname_3.25_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./ncurses-bin_6.5%2b20250216-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libcrypt1_4.4.38-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./perl-base_5.40.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./sed_4.9-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libaudit-common_4.0.2-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libcap-ng0_0.8.5-4%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libaudit1_4.0.2-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libdb5.3t64_5.3.28%2bdfsg2-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./debconf_1.5.91_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libpam0g_1.7.0-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libpam-modules-bin_1.7.0-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libpam-modules_1.7.0-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libpam-runtime_1.7.0-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libblkid1_2.41-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libsqlite3-0_3.46.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./liblastlog2-2_2.41-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libmount1_2.41-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libsmartcols1_2.41-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libudev1_257.5-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libuuid1_2.41-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./util-linux_2.41-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libdebconfclient0_0.278_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./base-passwd_3.6.7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./init-system-helpers_1.68_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./libc-bin_2.41-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./ncurses-base_6.5%2b20250216-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:49] "GET /./sysvinit-utils_3.14-4_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.mE5o4mom7e 127.0.0.1 - - [02/Sep/2025 19:26:51] code 404, message File not found 127.0.0.1 - - [02/Sep/2025 19:26:51] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:41641 ./ InRelease 127.0.0.1 - - [02/Sep/2025 19:26:51] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:41641 ./ Release 127.0.0.1 - - [02/Sep/2025 19:26:51] code 404, message File not found 127.0.0.1 - - [02/Sep/2025 19:26:51] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:41641 ./ 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.mE5o4mom7e 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 - - [02/Sep/2025 19:26:55] "GET /./liblocale-gettext-perl_1.07-7%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./sensible-utils_0.0.24_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libstdc%2b%2b6_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libuchardet0_0.0.8-1%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./groff-base_1.23.0-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./bsdextrautils_2.41-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libgdbm6t64_1.24-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libpipeline1_1.5.8-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libseccomp2_2.6.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./man-db_2.13.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./bzip2_1.0.8-6_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libmagic-mgc_5.46-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libmagic1t64_5.46-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./file_5.46-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./gettext-base_0.23.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./perl-modules-5.40_5.40.1-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libgdbm-compat4t64_1.24-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libperl5.40_5.40.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./perl_5.40.1-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./xz-utils_5.8.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./m4_1.4.19-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./autoconf_2.72-3.1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./autotools-dev_20240727.1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./automake_1.17-4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./autopoint_0.23.1-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libsframe1_2.44-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./binutils-common_2.44-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libbinutils_2.44-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libgprofng0_2.44-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libctf-nobfd0_2.44-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libctf0_2.44-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libjansson4_2.14-2%2bb3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./binutils-x86-64-linux-gnu_2.44-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./binutils_2.44-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libc-dev-bin_2.41-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./linux-libc-dev_6.12.22-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libcrypt-dev_4.4.38-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./rpcsvc-proto_1.4.3-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libc6-dev_2.41-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libisl23_0.27-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libmpfr6_4.2.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libmpc3_1.3.1-1%2bb3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./cpp-14-x86-64-linux-gnu_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./cpp-14_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./cpp-x86-64-linux-gnu_14.2.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./cpp_14.2.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libcc1-0_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libgomp1_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libitm1_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libatomic1_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libasan8_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./liblsan0_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libtsan2_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libubsan1_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libhwasan0_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libquadmath0_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libgcc-14-dev_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./gcc-14-x86-64-linux-gnu_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./gcc-14_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./gcc-x86-64-linux-gnu_14.2.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./gcc_14.2.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./libstdc%2b%2b-14-dev_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:55] "GET /./g%2b%2b-14-x86-64-linux-gnu_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./g%2b%2b-14_14.2.0-19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./g%2b%2b-x86-64-linux-gnu_14.2.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./g%2b%2b_14.2.0-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./make_4.4.1-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./libdpkg-perl_1.22.18_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./patch_2.8-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./dpkg-dev_1.22.18_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./build-essential_12.12_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./libdebhelper-perl_13.24.2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./libtool_2.5.4-4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./dh-autoreconf_20_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./libarchive-zip-perl_1.68-1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./libfile-stripnondeterminism-perl_1.14.1-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./dh-strip-nondeterminism_1.14.1-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./libelf1t64_0.192-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./dwz_0.15-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./libunistring5_1.3-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./libxml2_2.12.7%2bdfsg%2breally2.9.14-0.4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./gettext_0.23.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./intltool-debian_0.35.0%2b20060710.6_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./po-debconf_1.0.21%2bnmu1_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./debhelper_13.24.2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./help2man_1.49.3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./libsimde-dev_0.8.2-3_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./zlib1g-dev_1.3.dfsg%2breally1.3.1-1%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [02/Sep/2025 19:26:56] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmpd4pzpjqq/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.mE5o4mom7e Reading package lists... Building dependency tree... Reading state information... openssl-provider-legacy is already the newest version (3.5.0-1). libaudit1 is already the newest version (1:4.0.2-2+b2). libmpc3 is already the newest version (1.3.1-1+b3). libmpc3 set to manually installed. gzip is already the newest version (1.13-1). libctf0 is already the newest version (2.44-3). libctf0 set to manually installed. libgmp10 is already the newest version (2:6.3.0+dfsg-3). liblzma5 is already the newest version (5.8.1-1). libsystemd0 is already the newest version (257.5-2). libblkid1 is already the newest version (2.41-4). help2man is already the newest version (1.49.3). help2man set to manually installed. ncurses-base is already the newest version (6.5+20250216-2). hostname is already the newest version (3.25). libisl23 is already the newest version (0.27-1). libisl23 set to manually installed. build-essential is already the newest version (12.12). build-essential set to manually installed. libstdc++-14-dev is already the newest version (14.2.0-19). libstdc++-14-dev set to manually installed. tar is already the newest version (1.35+dfsg-3.1). gettext-base is already the newest version (0.23.1-1). gettext-base set to manually installed. binutils-common is already the newest version (2.44-3). binutils-common set to manually installed. g++-14-x86-64-linux-gnu is already the newest version (14.2.0-19). g++-14-x86-64-linux-gnu set to manually installed. libgcc-s1 is already the newest version (14.2.0-19). libunistring5 is already the newest version (1.3-2). libunistring5 set to manually installed. autopoint is already the newest version (0.23.1-1). autopoint set to manually installed. libmount1 is already the newest version (2.41-4). libseccomp2 is already the newest version (2.6.0-2). libseccomp2 set to manually installed. libfile-stripnondeterminism-perl is already the newest version (1.14.1-2). libfile-stripnondeterminism-perl set to manually installed. po-debconf is already the newest version (1.0.21+nmu1). po-debconf set to manually installed. bash is already the newest version (5.2.37-2). libperl5.40 is already the newest version (5.40.1-3). libperl5.40 set to manually installed. dpkg-dev is already the newest version (1.22.18). dpkg-dev set to manually installed. xz-utils is already the newest version (5.8.1-1). xz-utils set to manually installed. libpam-modules is already the newest version (1.7.0-3). libgomp1 is already the newest version (14.2.0-19). libgomp1 set to manually installed. bsdextrautils is already the newest version (2.41-4). bsdextrautils set to manually installed. g++ is already the newest version (4:14.2.0-1). g++ set to manually installed. libxml2 is already the newest version (2.12.7+dfsg+really2.9.14-0.4). libxml2 set to manually installed. libssl3t64 is already the newest version (3.5.0-1). libzstd1 is already the newest version (1.5.7+dfsg-1). dpkg is already the newest version (1.22.18). libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libatomic1 is already the newest version (14.2.0-19). libatomic1 set to manually installed. bsdutils is already the newest version (1:2.41-4). libmd0 is already the newest version (1.1.0-2+b1). dh-strip-nondeterminism is already the newest version (1.14.1-2). dh-strip-nondeterminism set to manually installed. debhelper is already the newest version (13.24.2). debhelper set to manually installed. libitm1 is already the newest version (14.2.0-19). libitm1 set to manually installed. g++-14 is already the newest version (14.2.0-19). g++-14 set to manually installed. make is already the newest version (4.4.1-2). make set to manually installed. autoconf is already the newest version (2.72-3.1). autoconf set to manually installed. patch is already the newest version (2.8-1). patch set to manually installed. libgprofng0 is already the newest version (2.44-3). libgprofng0 set to manually installed. libtool is already the newest version (2.5.4-4). libtool set to manually installed. libdpkg-perl is already the newest version (1.22.18). libdpkg-perl set to manually installed. debianutils is already the newest version (5.22). dash is already the newest version (0.5.12-12). libdb5.3t64 is already the newest version (5.3.28+dfsg2-9). libsmartcols1 is already the newest version (2.41-4). gcc-x86-64-linux-gnu is already the newest version (4:14.2.0-1). gcc-x86-64-linux-gnu set to manually installed. libpcre2-8-0 is already the newest version (10.45-1). m4 is already the newest version (1.4.19-7). m4 set to manually installed. findutils is already the newest version (4.10.0-3). libcc1-0 is already the newest version (14.2.0-19). libcc1-0 set to manually installed. libacl1 is already the newest version (2.3.2-2+b1). cpp-x86-64-linux-gnu is already the newest version (4:14.2.0-1). cpp-x86-64-linux-gnu set to manually installed. groff-base is already the newest version (1.23.0-7). groff-base set to manually installed. libpam-runtime is already the newest version (1.7.0-3). libgcc-14-dev is already the newest version (14.2.0-19). libgcc-14-dev set to manually installed. ncurses-bin is already the newest version (6.5+20250216-2). gcc-14 is already the newest version (14.2.0-19). gcc-14 set to manually installed. libsimde-dev is already the newest version (0.8.2-3). libsimde-dev set to manually installed. zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.1-1+b1). zlib1g-dev set to manually installed. gcc-14-x86-64-linux-gnu is already the newest version (14.2.0-19). gcc-14-x86-64-linux-gnu set to manually installed. intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. libasan8 is already the newest version (14.2.0-19). libasan8 set to manually installed. libgdbm6t64 is already the newest version (1.24-2). libgdbm6t64 set to manually installed. bzip2 is already the newest version (1.0.8-6). bzip2 set to manually installed. libcrypt1 is already the newest version (1:4.4.38-1). libbinutils is already the newest version (2.44-3). libbinutils set to manually installed. linux-libc-dev is already the newest version (6.12.22-1). linux-libc-dev set to manually installed. sensible-utils is already the newest version (0.0.24). sensible-utils set to manually installed. libuuid1 is already the newest version (2.41-4). libdebhelper-perl is already the newest version (13.24.2). libdebhelper-perl set to manually installed. libjansson4 is already the newest version (2.14-2+b3). libjansson4 set to manually installed. libsframe1 is already the newest version (2.44-3). libsframe1 set to manually installed. dh-autoreconf is already the newest version (20). dh-autoreconf set to manually installed. autotools-dev is already the newest version (20240727.1). autotools-dev set to manually installed. libuchardet0 is already the newest version (0.0.8-1+b2). libuchardet0 set to manually installed. man-db is already the newest version (2.13.0-1). man-db set to manually installed. sysvinit-utils is already the newest version (3.14-4). libstdc++6 is already the newest version (14.2.0-19). libstdc++6 set to manually installed. binutils is already the newest version (2.44-3). binutils set to manually installed. gcc-14-base is already the newest version (14.2.0-19). zlib1g is already the newest version (1:1.3.dfsg+really1.3.1-1+b1). libcap-ng0 is already the newest version (0.8.5-4+b1). dwz is already the newest version (0.15-1+b1). dwz set to manually installed. init-system-helpers is already the newest version (1.68). libmagic-mgc is already the newest version (1:5.46-5). libmagic-mgc set to manually installed. mawk is already the newest version (1.3.4.20250131-1). libelf1t64 is already the newest version (0.192-4). libelf1t64 set to manually installed. file is already the newest version (1:5.46-5). file set to manually installed. libattr1 is already the newest version (1:2.5.2-3). libdebconfclient0 is already the newest version (0.278). libubsan1 is already the newest version (14.2.0-19). libubsan1 set to manually installed. libtsan2 is already the newest version (14.2.0-19). libtsan2 set to manually installed. libc-bin is already the newest version (2.41-7). perl-base is already the newest version (5.40.1-3). libc6-dev is already the newest version (2.41-7). libc6-dev set to manually installed. libpam0g is already the newest version (1.7.0-3). liblocale-gettext-perl is already the newest version (1.07-7+b1). liblocale-gettext-perl set to manually installed. sed is already the newest version (4.9-2). g++-x86-64-linux-gnu is already the newest version (4:14.2.0-1). g++-x86-64-linux-gnu set to manually installed. gettext is already the newest version (0.23.1-1). gettext set to manually installed. libquadmath0 is already the newest version (14.2.0-19). libquadmath0 set to manually installed. base-files is already the newest version (13.7). libc-dev-bin is already the newest version (2.41-7). libc-dev-bin set to manually installed. util-linux is already the newest version (2.41-4). libtinfo6 is already the newest version (6.5+20250216-2). cpp-14-x86-64-linux-gnu is already the newest version (14.2.0-19). cpp-14-x86-64-linux-gnu set to manually installed. libc6 is already the newest version (2.41-7). grep is already the newest version (3.11-4). cpp-14 is already the newest version (14.2.0-19). cpp-14 set to manually installed. debconf is already the newest version (1.5.91). libselinux1 is already the newest version (3.8.1-1). base-passwd is already the newest version (3.6.7). libudev1 is already the newest version (257.5-2). gcc is already the newest version (4:14.2.0-1). gcc set to manually installed. libctf-nobfd0 is already the newest version (2.44-3). libctf-nobfd0 set to manually installed. libsqlite3-0 is already the newest version (3.46.1-3). libpipeline1 is already the newest version (1.5.8-1). libpipeline1 set to manually installed. libaudit-common is already the newest version (1:4.0.2-2). diffutils is already the newest version (1:3.10-3). libbz2-1.0 is already the newest version (1.0.8-6). liblsan0 is already the newest version (14.2.0-19). liblsan0 set to manually installed. libmpfr6 is already the newest version (4.2.2-1). libmpfr6 set to manually installed. perl-modules-5.40 is already the newest version (5.40.1-3). perl-modules-5.40 set to manually installed. libpam-modules-bin is already the newest version (1.7.0-3). liblastlog2-2 is already the newest version (2.41-4). libgdbm-compat4t64 is already the newest version (1.24-2). libgdbm-compat4t64 set to manually installed. cpp is already the newest version (4:14.2.0-1). cpp set to manually installed. libcrypt-dev is already the newest version (1:4.4.38-1). libcrypt-dev set to manually installed. coreutils is already the newest version (9.7-1). libmagic1t64 is already the newest version (1:5.46-5). libmagic1t64 set to manually installed. libhwasan0 is already the newest version (14.2.0-19). libhwasan0 set to manually installed. libcap2 is already the newest version (1:2.75-6). binutils-x86-64-linux-gnu is already the newest version (2.44-3). binutils-x86-64-linux-gnu set to manually installed. perl is already the newest version (5.40.1-3). perl set to manually installed. rpcsvc-proto is already the newest version (1.4.3-1). rpcsvc-proto set to manually installed. automake is already the newest version (1:1.17-4). automake set to manually installed. 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.mE5o4mom7e (Reading database ... 14020 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.mE5o4mom7e I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.mE5o4mom7e 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.mE5o4mom7e... I: success in 19.0011 seconds Downloading dependency 136 of 147: liblastlog2-2:amd64=2.41-4 Downloading dependency 137 of 147: libgdbm-compat4t64:amd64=1.24-2 Downloading dependency 138 of 147: cpp:amd64=4:14.2.0-1 Downloading dependency 139 of 147: libcrypt-dev:amd64=1:4.4.38-1 Downloading dependency 140 of 147: coreutils:amd64=9.7-1 Downloading dependency 141 of 147: libmagic1t64:amd64=1:5.46-5 Downloading dependency 142 of 147: libhwasan0:amd64=14.2.0-19 Downloading dependency 143 of 147: libcap2:amd64=1:2.75-6 Downloading dependency 144 of 147: binutils-x86-64-linux-gnu:amd64=2.44-3 Downloading dependency 145 of 147: perl:amd64=5.40.1-3 Downloading dependency 146 of 147: rpcsvc-proto:amd64=1.4.3-1 Downloading dependency 147 of 147: automake:amd64=1:1.17-4 env --chdir=/srv/rebuilderd/tmp/rebuilderdS6PC0H/out DEB_BUILD_OPTIONS=parallel=6 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1744881086 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildo6jZu5/debrebuild.sbuildrc.Ziqv6fiZ7_RN sbuild --build=amd64 --host=amd64 --no-source --arch-any --no-arch-all --binNMU-changelog= bwa-mem2 (2.2.1-1+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild on buildd -- amd64 Build Daemon (x86-grnet-01) Thu, 17 Apr 2025 09:11:26 +0000 --chroot=/srv/rebuilderd/tmp/debrebuildo6jZu5/debrebuild.tar.NlogNDRQCT4a --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-mem2-2.2.1 /srv/rebuilderd/tmp/rebuilderdS6PC0H/inputs/bwa-mem2_2.2.1-1.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: warning: descr(l1): found blank line where expected first heading sbuild (Debian sbuild) 0.89.3 (07 June 2025) on osuosl4-amd64.reproducible.osuosl.org +==============================================================================+ | bwa-mem2 2.2.1-1+b1 (amd64) Tue, 02 Sep 2025 19:27:08 +0000 | +==============================================================================+ Package: bwa-mem2 Version: 2.2.1-1+b1 Source Version: 2.2.1-1 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/debrebuildo6jZu5/debrebuild.tar.NlogNDRQCT4a to /srv/rebuilderd/tmp/tmp.sbuild.Ua7RVX7PbU... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Tue, 02 Sep 2025 19:27:13 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdS6PC0H/inputs/bwa-mem2_2.2.1-1.dsc exists in /srv/rebuilderd/tmp/rebuilderdS6PC0H/inputs; copying to chroot sbuild: warning: descr(l1): found blank line where expected first heading +------------------------------------------------------------------------------+ | Install package build dependencies Tue, 02 Sep 2025 19:27:15 +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-r89OOm/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Tue, 02 Sep 2025 19:27:18 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Tue, 02 Sep 2025 19:27:19 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) amd64 (x86_64) Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.18 g++-14_14.2.0-19 gcc-14_14.2.0-19 libc6-dev_2.41-7 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 linux-libc-dev_6.12.22-1 Package versions: autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-1 autotools-dev_20240727.1 base-files_13.7 base-passwd_3.6.7 bash_5.2.37-2 binutils_2.44-3 binutils-common_2.44-3 binutils-x86-64-linux-gnu_2.44-3 bsdextrautils_2.41-4 bsdutils_1:2.41-4 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.7-1 cpp_4:14.2.0-1 cpp-14_14.2.0-19 cpp-14-x86-64-linux-gnu_14.2.0-19 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.24.2 debianutils_5.22 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-3 dpkg_1.22.18 dpkg-dev_1.22.18 dwz_0.15-1+b1 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.2.0-19 g++-14-x86-64-linux-gnu_14.2.0-19 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-19 gcc-14-base_14.2.0-19 gcc-14-x86-64-linux-gnu_14.2.0-19 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-1 gettext-base_0.23.1-1 grep_3.11-4 groff-base_1.23.0-7 gzip_1.13-1 help2man_1.49.3 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libarchive-zip-perl_1.68-1 libasan8_14.2.0-19 libatomic1_14.2.0-19 libattr1_1:2.5.2-3 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b2 libbinutils_2.44-3 libblkid1_2.41-4 libbz2-1.0_1.0.8-6 libc-bin_2.41-7 libc-dev-bin_2.41-7 libc6_2.41-7 libc6-dev_2.41-7 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-6 libcc1-0_14.2.0-19 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.278 libdebhelper-perl_13.24.2 libdpkg-perl_1.22.18 libelf1t64_0.192-4 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-14-dev_14.2.0-19 libgcc-s1_14.2.0-19 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp10_2:6.3.0+dfsg-3 libgomp1_14.2.0-19 libgprofng0_2.44-3 libhwasan0_14.2.0-19 libisl23_0.27-1 libitm1_14.2.0-19 libjansson4_2.14-2+b3 liblastlog2-2_2.41-4 liblocale-gettext-perl_1.07-7+b1 liblsan0_14.2.0-19 liblzma5_5.8.1-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41-4 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 libpam-modules_1.7.0-3 libpam-modules-bin_1.7.0-3 libpam-runtime_1.7.0-3 libpam0g_1.7.0-3 libpcre2-8-0_10.45-1 libperl5.40_5.40.1-3 libpipeline1_1.5.8-1 libquadmath0_14.2.0-19 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsframe1_2.44-3 libsimde-dev_0.8.2-3 libsmartcols1_2.41-4 libsqlite3-0_3.46.1-3 libssl3t64_3.5.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 libsystemd0_257.5-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_14.2.0-19 libubsan1_14.2.0-19 libuchardet0_0.0.8-1+b2 libudev1_257.5-2 libunistring5_1.3-2 libuuid1_2.41-4 libxml2_2.12.7+dfsg+really2.9.14-0.4 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.22-1 m4_1.4.19-7 make_4.4.1-2 man-db_2.13.0-1 mawk_1.3.4.20250131-1 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 openssl-provider-legacy_3.5.0-1 patch_2.8-1 perl_5.40.1-3 perl-base_5.40.1-3 perl-modules-5.40_5.40.1-3 po-debconf_1.0.21+nmu1 rpcsvc-proto_1.4.3-1 sed_4.9-2 sensible-utils_0.0.24 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 util-linux_2.41-4 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Tue, 02 Sep 2025 19:27:19 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bwa-mem2 Binary: bwa-mem2 Architecture: any Version: 2.2.1-1 Maintainer: Debian Med Packaging Team Uploaders: Dylan Aïssi , Michael R. Crusoe Homepage: https://github.com/bwa-mem2/bwa-mem2 Standards-Version: 4.6.0 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: de5a55bb0efe3fa7242752b7d466581f0078f4ac 230828 bwa-mem2_2.2.1.orig.tar.xz 7980e0bc0fe26272dd9feb2f91af41a5e1abfbde 26796 bwa-mem2_2.2.1-1.debian.tar.xz Checksums-Sha256: 75c67d795f79fd3a3a42dd655aec3e6aee3ac231d46a5ae7214e2448df0ce450 230828 bwa-mem2_2.2.1.orig.tar.xz ba3e5b966151d9d1af0ab13a45949420f350d422e872eb6ccb0050fc1b167816 26796 bwa-mem2_2.2.1-1.debian.tar.xz Files: e68e6cd8575d8158539dbaed8ab4b6f2 230828 bwa-mem2_2.2.1.orig.tar.xz 64219192c0dcec9d2d5e6e7d3a823e71 26796 bwa-mem2_2.2.1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmf/p/kACgkQPCZ2P2xn 5uJLJhAApATg6bKDkr2mUEJ16WdQXTrwPCQDCf88lQmVaxKUfjVuiGfOi7Gbg20e X3WuGzUAhmatOk6tUvyAFfneVuUNeiRTptpUPLpG1ArlqGAFcW1ixMkyFjb42jnU 5rIpNR8rJdmWA3GRIcNImXY2dNEGxIf9TfD58YZpc39aHHBCEe+uQzsz4180MptO YRON9hDmLhutNALoum9wAuGkJLuVaqja80irD1d9R9Zq+Tb7ZV1K153kVAVM3kSX Pz0VZL09ZMbr6XxBNJ94IHmN/1JSH8vFbR2WFu7ko5jXCnDnEAxHigIs5Y1tH35l YFPY7a+KhutNpsF1zjGcvS4MLhDbKiNI6EcYLLjvYAOAJfLRgjUjgsh/MY8YrGiV fAhGcaTvODddTO01UBCGFiR1hEpHh/vnFmgbq9GSG7LI4c7O55MxOLwWnIcp1XTT F1SxDYyISlwiQoib5WRmEQZlmA3CQ3APTdf3bgNDxkmPs0q1KnN8YpoXaRsD94gz PArWcNzj3Q823s3CdMHNtdJMWY7qNxRQf7wtPoNef/qHzsjBzalEl7UzcdQeF6uW A9Ggp4C1KZ4l++UBGOwAtrhN6RzeRbQ4aC44KXTKOErVaWYS6P/7c1e8a8xH2OV7 GAD/PCwRH1ko0aHYXSo5LE+YyQ+ArNiuZdeZSraSD84+j0KXL0U= =2M5K -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./bwa-mem2_2.2.1-1.dsc: unsupported subcommand dpkg-source: info: extracting bwa-mem2 in /build/reproducible-path/bwa-mem2-2.2.1 dpkg-source: info: unpacking bwa-mem2_2.2.1.orig.tar.xz dpkg-source: info: unpacking bwa-mem2_2.2.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-Fix-typo.patch dpkg-source: info: applying 0002-fixed-return-status-due-incorrect-input-files.patch dpkg-source: info: applying 0003-fixed-smem-memory-rellocation-issue-issue167.patch dpkg-source: info: applying 0004-Update-to-reflect-2.2.1-release-and-small-typo.patch dpkg-source: info: applying 0005-GCC-11-now-defines-__rdtsc-so-definition-test-condit.patch dpkg-source: info: applying 0006-fixed-segfault-due-to-memory-shortage-in-smem.patch dpkg-source: info: applying 0007-Merge-pull-request-229-from-gh-jphan-fix_n_processed.patch 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 Hack binNMU version ------------------- Created changelog entry for binNMU version 2.2.1-1+b1 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=1744881086 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -B dpkg-buildpackage: info: source package bwa-mem2 dpkg-buildpackage: info: source version 2.2.1-1+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 Build Daemon (x86-grnet-01) 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-mem2-2.2.1' dh_auto_clean || true make -j6 clean make[2]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' 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-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make[2]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' make[1]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' 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-mem2-2.2.1' 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-mem2-2.2.1' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=sse41 EXE=bwa-mem2.sse41 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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) | ^~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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 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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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/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-mem2-2.2.1=. -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/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/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: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:654:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 654 | fprintf(stderr, "[%0.4d] REA Re-allocating enc_qdb only\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:730:57: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:59: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | 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:1006:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1006 | 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:1370:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1370 | 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:1842:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1842 | 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:2237:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2237 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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: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/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__); | ^~~~~~~~ cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' 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 ()); | ~~~~~~~~~~~~~~~~~ make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1=. -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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/strtouppercase_s.o safeclib/strtouppercase_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1/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-mem2-2.2.1=. -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-mem2-2.2.1' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=sse42 EXE=bwa-mem2.sse42 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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: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__); | ^~~~~~~~ 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__); | ^~~~~~~~ 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: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:654:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 654 | fprintf(stderr, "[%0.4d] REA Re-allocating enc_qdb only\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:730:57: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:59: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | 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:1006:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1006 | 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:1370:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1370 | 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:1842:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1842 | 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:2237:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2237 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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/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-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1=. -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/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-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/strlastsame_s.o safeclib/strlastsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1/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-mem2-2.2.1=. -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-mem2-2.2.1' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=avx EXE=bwa-mem2.avx CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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 g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 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) | ^~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 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/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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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__); | ^~~~~~~~ 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/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/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__); | ^~~~~~~~ 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-mem2-2.2.1=. -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: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:654:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 654 | fprintf(stderr, "[%0.4d] REA Re-allocating enc_qdb only\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:730:57: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:59: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | 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:1006:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1006 | 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:1370:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1370 | 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:1842:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1842 | 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:2237:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2237 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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/strlastsame_s.o safeclib/strlastsame_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1/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-mem2-2.2.1=. -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-mem2-2.2.1' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=avx2 EXE=bwa-mem2.avx2 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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) | ^~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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 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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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/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_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: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:654:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 654 | fprintf(stderr, "[%0.4d] REA Re-allocating enc_qdb only\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:730:57: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:59: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | 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:1006:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1006 | 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:1370:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1370 | 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-mem2-2.2.1=. -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.cpp: In function ‘void* _mm_realloc(void*, int64_t, int64_t, int16_t)’: src/bwamem.cpp:1842:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1842 | 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:2237:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2237 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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/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-mem2-2.2.1=. -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-mem2-2.2.1=. -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/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-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1=. -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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/strcasestr_s.o safeclib/strcasestr_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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/memmove16_s.o safeclib/memmove16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1/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-mem2-2.2.1=. -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-mem2-2.2.1' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=avx512 EXE=bwa-mem2.avx512bw CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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) | ^~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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 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/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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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/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: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: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) | ^~~~~~~~~~ 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.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__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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.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:654:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 654 | fprintf(stderr, "[%0.4d] REA Re-allocating enc_qdb only\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:730:57: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:59: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | 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:1006:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1006 | 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:1370:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1370 | 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:1842:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1842 | 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:2237:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2237 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-mem2-2.2.1=. -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 g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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: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 ‘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-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1=. -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/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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/wcsncpy_s.o safeclib/wcsncpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1/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-mem2-2.2.1=. -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-mem2-2.2.1' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1' dh_auto_build -- multi make -j6 "INSTALL=install --strip-program=true" multi make[2]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=sse41 EXE=bwa-mem2.sse41 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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 g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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 g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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_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/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-mem2-2.2.1=. -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 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-mem2-2.2.1=. -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 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) | ^~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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/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:654:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 654 | fprintf(stderr, "[%0.4d] REA Re-allocating enc_qdb only\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:730:57: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:59: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | 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:1006:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1006 | 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:1370:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1370 | memcpy_bwamem(pes, 4 * sizeof(mem_pestat_t), pes0, 4 * sizeof(mem_pestat_t), __FILE__, __LINE__); // if pes0 != NULL, set the insert-size | ^~~~~~~~ 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/bwamem.cpp: In function ‘void* _mm_realloc(void*, int64_t, int64_t, int16_t)’: src/bwamem.cpp:1842:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1842 | 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:2237:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2237 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1=. -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/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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/strljustify_s.o safeclib/strljustify_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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/strpbrk_s.o safeclib/strpbrk_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1/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-mem2-2.2.1=. -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-mem2-2.2.1' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=sse42 EXE=bwa-mem2.sse42 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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/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) | ^~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 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/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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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 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-mem2-2.2.1=. -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 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) | ^~~~~~~~~~ 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/ksort.h:78:52: warning: ISO C++17 does not allow ‘register’ 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:654:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 654 | fprintf(stderr, "[%0.4d] REA Re-allocating enc_qdb only\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:730:57: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:59: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | 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:1006:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1006 | 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:1370:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1370 | 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:1842:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1842 | memcpy_bwamem(nptr, nsize * dsize, ptr, csize, __FILE__, __LINE__); | ^~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 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:2237:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2237 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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_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_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-mem2-2.2.1=. -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/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-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1=. -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 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/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1/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-mem2-2.2.1=. -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-mem2-2.2.1' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=avx EXE=bwa-mem2.avx CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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 g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 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) | ^~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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 g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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/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-mem2-2.2.1=. -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 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/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: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) | ^~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 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:654:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 654 | fprintf(stderr, "[%0.4d] REA Re-allocating enc_qdb only\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:730:57: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:59: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | 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:1006:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1006 | 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:1370:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1370 | 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:1842:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1842 | 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:2237:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2237 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-mem2-2.2.1=. -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 g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1=. -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/stpcpy_s.o safeclib/stpcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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/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/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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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/memcmp16_s.o safeclib/memcmp16_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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/strfirstchar_s.o safeclib/strfirstchar_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1/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-mem2-2.2.1=. -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-mem2-2.2.1' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=avx2 EXE=bwa-mem2.avx2 CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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 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) | ^~~~~~~~~~ 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__); | ^~~~~~~~ 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-mem2-2.2.1=. -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 g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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/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:654:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 654 | fprintf(stderr, "[%0.4d] REA Re-allocating enc_qdb only\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:730:57: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:59: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 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:1006:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1006 | 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:1370:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1370 | 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:1842:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1842 | 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:2237:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2237 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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_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-mem2-2.2.1=. -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/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__); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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_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-mem2-2.2.1=. -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__); | ^~~~~~~~ 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-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1=. -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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/strcpy_s.o safeclib/strcpy_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1/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-mem2-2.2.1=. -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-mem2-2.2.1' rm -f src/*.o libbwa.a; cd ext/safestringlib/ && make clean; make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make arch=avx512 EXE=bwa-mem2.avx512bw CXX=g++ all make[3]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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/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) | ^~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 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-mem2-2.2.1=. -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-mem2-2.2.1=. -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-mem2-2.2.1=. -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 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-mem2-2.2.1=. -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 g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 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-mem2-2.2.1=. -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-mem2-2.2.1=. -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 g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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 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-mem2-2.2.1=. -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 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: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:654:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 654 | fprintf(stderr, "[%0.4d] REA Re-allocating enc_qdb only\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:686:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 686 | fprintf(stderr, "[%0.4d] REA Re-allocating min_intv, query_pos, & rid\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:723:29: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 723 | fprintf(stderr, "[%0.4d] REA Re-allocating2 SMEM data structures due to enc_qdb\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:730:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:730:57: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 730 | fprintf(stderr, "Realloc size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~~~~~~~~~~~~~~~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:59: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | fprintf(stderr, "Realloc2 size from: %d to :%d\n", tmp, mmc->wsize_mem[tid]); | ~^ ~~~ | | | | int int64_t {aka long int} | %ld src/bwamem.cpp:765:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=] 765 | 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:1006:25: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 1006 | 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:1370:90: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1370 | 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:1842:52: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 1842 | 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:2237:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2237 | fprintf(stderr, "[0000][%0.4d] Re-allocating seqPairArrays, in Left\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2260:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2260 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2280:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2280 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (left)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2333:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2333 | fprintf(stderr, "[0000] [%0.4d] Re-allocating seqPairArrays Right\n", tid); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2358:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2358 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufQers in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/bwamem.cpp:2374:41: warning: '0' flag ignored with precision and ‘%d’ gnu_printf format [-Wformat=] 2374 | fprintf(stderr, "[%0.4d] Re-allocating (doubling) seqBufRefs in %s (right)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-mem2-2.2.1=. -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__); | ^~~~~~~~ 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-mem2-2.2.1=. -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 cd ext/safestringlib/ && make clean && make CC=gcc directories libsafestring.a make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' rm -f obj/*.o *~ core /*~ objtest/*.o rm -f libsafestring.a rm -f safestringtest 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__); | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1/ext/safestringlib' make[4]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1/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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1=. -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/ignore_handler_s.o safeclib/ignore_handler_s.c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -DSTDC_HEADERS gcc -Wdate-time -D_FORTIFY_SOURCE=2 -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 -DSAIS=1 -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-mem2-2.2.1=. -fstack-protector-strong -fstack-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-mem2-2.2.1/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-mem2-2.2.1=. -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-mem2-2.2.1' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bwa-mem2-2.2.1=. -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-mem2-2.2.1' help2man --no-discard-stderr --version-string="2.2.1" \ --help-option=' ' --no-info ./bwa-mem2 --name="Sequence alignment using Burrows-Wheeler Transform" \ > debian/bwa-mem2.1 help2man --no-discard-stderr --version-string="2.2.1" \ --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-mem2-2.2.1' 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_2.2.1-1+b1_amd64.deb'. dpkg-deb: building package 'bwa-mem2-dbgsym' in '../bwa-mem2-dbgsym_2.2.1-1+b1_amd64.deb'. dpkg-genbuildinfo --build=any -O../bwa-mem2_2.2.1-1+b1_amd64.buildinfo dpkg-genchanges --build=any -O../bwa-mem2_2.2.1-1+b1_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 2025-09-02T19:29:20Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Tue, 02 Sep 2025 19:29:21 +0000 | +------------------------------------------------------------------------------+ bwa-mem2_2.2.1-1+b1_amd64.changes: ---------------------------------- Format: 1.8 Date: Thu, 17 Apr 2025 09:11:26 +0000 Source: bwa-mem2 (2.2.1-1) Binary: bwa-mem2 bwa-mem2-dbgsym Binary-Only: yes Architecture: amd64 Version: 2.2.1-1+b1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team Changed-By: amd64 Build Daemon (x86-grnet-01) Description: bwa-mem2 - Sequence alignment using Burrows-Wheeler Transform Changes: bwa-mem2 (2.2.1-1+b1) sid; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild on buildd Checksums-Sha1: 63c9f75890253911c83749b62dcb4fb615112885 2017640 bwa-mem2-dbgsym_2.2.1-1+b1_amd64.deb 569aff4566723dbd450d3bd2586c23634b500e1f 5238 bwa-mem2_2.2.1-1+b1_amd64.buildinfo ed2af6ced027a7f9753483b9b3765d642479e561 368536 bwa-mem2_2.2.1-1+b1_amd64.deb Checksums-Sha256: fd46fa7e9d95dd3c729aae111352077514daac1e0fe34b17c1dc1ab3c47b9790 2017640 bwa-mem2-dbgsym_2.2.1-1+b1_amd64.deb 1283a6714380152f25299cdb030b6d70321cbbeaeb71615df403459f83e30ec6 5238 bwa-mem2_2.2.1-1+b1_amd64.buildinfo 5b69c447703265cf958aecd9d40cc8ea20615953fe0f37a113618f1178f24a0c 368536 bwa-mem2_2.2.1-1+b1_amd64.deb Files: dcfd19cac056faa6d6b3b887b9bccd3b 2017640 debug optional bwa-mem2-dbgsym_2.2.1-1+b1_amd64.deb a22d9a94a9ea878b0ab984eca64f53db 5238 science optional bwa-mem2_2.2.1-1+b1_amd64.buildinfo 54be519f67bae66c5723833743c9aa7d 368536 science optional bwa-mem2_2.2.1-1+b1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Tue, 02 Sep 2025 19:29:22 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: bwa-mem2 (2.2.1-1) Binary: bwa-mem2 bwa-mem2-dbgsym Architecture: amd64 Version: 2.2.1-1+b1 Binary-Only-Changes: bwa-mem2 (2.2.1-1+b1) sid; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild on buildd . -- amd64 Build Daemon (x86-grnet-01) Thu, 17 Apr 2025 09:11:26 +0000 Checksums-Md5: dcfd19cac056faa6d6b3b887b9bccd3b 2017640 bwa-mem2-dbgsym_2.2.1-1+b1_amd64.deb 54be519f67bae66c5723833743c9aa7d 368536 bwa-mem2_2.2.1-1+b1_amd64.deb Checksums-Sha1: 63c9f75890253911c83749b62dcb4fb615112885 2017640 bwa-mem2-dbgsym_2.2.1-1+b1_amd64.deb ed2af6ced027a7f9753483b9b3765d642479e561 368536 bwa-mem2_2.2.1-1+b1_amd64.deb Checksums-Sha256: fd46fa7e9d95dd3c729aae111352077514daac1e0fe34b17c1dc1ab3c47b9790 2017640 bwa-mem2-dbgsym_2.2.1-1+b1_amd64.deb 5b69c447703265cf958aecd9d40cc8ea20615953fe0f37a113618f1178f24a0c 368536 bwa-mem2_2.2.1-1+b1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 02 Sep 2025 19:29:20 +0000 Build-Path: /build/reproducible-path/bwa-mem2-2.2.1 Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.17-4), autopoint (= 0.23.1-1), autotools-dev (= 20240727.1), base-files (= 13.7), base-passwd (= 3.6.7), bash (= 5.2.37-2), binutils (= 2.44-3), binutils-common (= 2.44-3), binutils-x86-64-linux-gnu (= 2.44-3), bsdextrautils (= 2.41-4), bsdutils (= 1:2.41-4), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.7-1), cpp (= 4:14.2.0-1), cpp-14 (= 14.2.0-19), cpp-14-x86-64-linux-gnu (= 14.2.0-19), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.24.2), debianutils (= 5.22), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-3), dpkg (= 1.22.18), dpkg-dev (= 1.22.18), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-19), g++-14-x86-64-linux-gnu (= 14.2.0-19), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-14 (= 14.2.0-19), gcc-14-base (= 14.2.0-19), gcc-14-x86-64-linux-gnu (= 14.2.0-19), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-1), gettext-base (= 0.23.1-1), grep (= 3.11-4), groff-base (= 1.23.0-7), gzip (= 1.13-1), help2man (= 1.49.3), hostname (= 3.25), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-19), libatomic1 (= 14.2.0-19), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.2-2), libaudit1 (= 1:4.0.2-2+b2), libbinutils (= 2.44-3), libblkid1 (= 2.41-4), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.41-7), libc-dev-bin (= 2.41-7), libc6 (= 2.41-7), libc6-dev (= 2.41-7), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-6), libcc1-0 (= 14.2.0-19), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.44-3), libctf0 (= 2.44-3), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.278), libdebhelper-perl (= 13.24.2), libdpkg-perl (= 1.22.18), libelf1t64 (= 0.192-4), libfile-stripnondeterminism-perl (= 1.14.1-2), libgcc-14-dev (= 14.2.0-19), libgcc-s1 (= 14.2.0-19), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp10 (= 2:6.3.0+dfsg-3), libgomp1 (= 14.2.0-19), libgprofng0 (= 2.44-3), libhwasan0 (= 14.2.0-19), libisl23 (= 0.27-1), libitm1 (= 14.2.0-19), libjansson4 (= 2.14-2+b3), liblastlog2-2 (= 2.41-4), liblocale-gettext-perl (= 1.07-7+b1), liblsan0 (= 14.2.0-19), liblzma5 (= 5.8.1-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41-4), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.2-1), libpam-modules (= 1.7.0-3), libpam-modules-bin (= 1.7.0-3), libpam-runtime (= 1.7.0-3), libpam0g (= 1.7.0-3), libpcre2-8-0 (= 10.45-1), libperl5.40 (= 5.40.1-3), libpipeline1 (= 1.5.8-1), libquadmath0 (= 14.2.0-19), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe1 (= 2.44-3), libsimde-dev (= 0.8.2-3), libsmartcols1 (= 2.41-4), libsqlite3-0 (= 3.46.1-3), libssl3t64 (= 3.5.0-1), libstdc++-14-dev (= 14.2.0-19), libstdc++6 (= 14.2.0-19), libsystemd0 (= 257.5-2), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 14.2.0-19), libubsan1 (= 14.2.0-19), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257.5-2), libunistring5 (= 1.3-2), libuuid1 (= 2.41-4), libxml2 (= 2.12.7+dfsg+really2.9.14-0.4), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.22-1), m4 (= 1.4.19-7), make (= 4.4.1-2), man-db (= 2.13.0-1), mawk (= 1.3.4.20250131-1), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), openssl-provider-legacy (= 3.5.0-1), patch (= 2.8-1), perl (= 5.40.1-3), perl-base (= 5.40.1-3), perl-modules-5.40 (= 5.40.1-3), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), util-linux (= 2.41-4), xz-utils (= 5.8.1-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=6" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1744881086" +------------------------------------------------------------------------------+ | Package contents Tue, 02 Sep 2025 19:29:22 +0000 | +------------------------------------------------------------------------------+ bwa-mem2-dbgsym_2.2.1-1+b1_amd64.deb ------------------------------------ new Debian package, version 2.0. size 2017640 bytes: control archive=860 bytes. 596 bytes, 12 lines control 721 bytes, 7 lines md5sums Package: bwa-mem2-dbgsym Source: bwa-mem2 (2.2.1-1) Version: 2.2.1-1+b1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2442 Depends: bwa-mem2 (= 2.2.1-1+b1) Section: debug Priority: optional Description: debug symbols for bwa-mem2 Build-Ids: 097cb5ff8dbac71db56fa9afcf83921690ce4c63 12e12515668e04a5f74be0468a2281b0b9f523e1 17c03b2610f005f895ed81ef2dede0843802e5bd 46c217db84da3a2894f0f5c1ac3c2d8d5e226380 9399a8f8ab8e4e0ab1c3a062a68bca74b0dc2110 c4952b12b731721889636a8362ae51b7e938f1d8 drwxr-xr-x root/root 0 2025-04-17 09:11 ./ drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/ drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/lib/ drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/lib/debug/.build-id/09/ -rw-r--r-- root/root 467648 2025-04-17 09:11 ./usr/lib/debug/.build-id/09/7cb5ff8dbac71db56fa9afcf83921690ce4c63.debug drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/lib/debug/.build-id/12/ -rw-r--r-- root/root 497568 2025-04-17 09:11 ./usr/lib/debug/.build-id/12/e12515668e04a5f74be0468a2281b0b9f523e1.debug drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/lib/debug/.build-id/17/ -rw-r--r-- root/root 472736 2025-04-17 09:11 ./usr/lib/debug/.build-id/17/c03b2610f005f895ed81ef2dede0843802e5bd.debug drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/lib/debug/.build-id/46/ -rw-r--r-- root/root 468560 2025-04-17 09:11 ./usr/lib/debug/.build-id/46/c217db84da3a2894f0f5c1ac3c2d8d5e226380.debug drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/lib/debug/.build-id/93/ -rw-r--r-- root/root 467200 2025-04-17 09:11 ./usr/lib/debug/.build-id/93/99a8f8ab8e4e0ab1c3a062a68bca74b0dc2110.debug drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/lib/debug/.build-id/c4/ -rw-r--r-- root/root 20872 2025-04-17 09:11 ./usr/lib/debug/.build-id/c4/952b12b731721889636a8362ae51b7e938f1d8.debug drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 85200 2025-04-17 09:11 ./usr/lib/debug/.dwz/x86_64-linux-gnu/bwa-mem2.debug drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/share/ drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-04-17 09:11 ./usr/share/doc/bwa-mem2-dbgsym -> bwa-mem2 bwa-mem2_2.2.1-1+b1_amd64.deb ----------------------------- new Debian package, version 2.0. size 368536 bytes: control archive=1372 bytes. 1057 bytes, 21 lines control 1137 bytes, 17 lines md5sums Package: bwa-mem2 Source: bwa-mem2 (2.2.1-1) Version: 2.2.1-1+b1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1763 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 2025-04-17 09:11 ./ drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/ drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/bin/ -rwxr-xr-x root/root 14568 2025-04-17 09:11 ./usr/bin/bwa-mem2 -rwxr-xr-x root/root 338584 2025-04-17 09:11 ./usr/bin/bwa-mem2.avx -rwxr-xr-x root/root 350872 2025-04-17 09:11 ./usr/bin/bwa-mem2.avx2 -rwxr-xr-x root/root 375448 2025-04-17 09:11 ./usr/bin/bwa-mem2.avx512bw -rwxr-xr-x root/root 346776 2025-04-17 09:11 ./usr/bin/bwa-mem2.sse41 -rwxr-xr-x root/root 346776 2025-04-17 09:11 ./usr/bin/bwa-mem2.sse42 drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/share/ drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/share/doc/bwa-mem2/ -rw-r--r-- root/root 1435 2021-03-17 05:38 ./usr/share/doc/bwa-mem2/NEWS.md.gz -rw-r--r-- root/root 3022 2025-04-17 09:11 ./usr/share/doc/bwa-mem2/README.md.gz -rw-r--r-- root/root 212 2025-04-17 09:11 ./usr/share/doc/bwa-mem2/changelog.Debian.amd64.gz -rw-r--r-- root/root 163 2025-04-17 09:11 ./usr/share/doc/bwa-mem2/changelog.Debian.gz -rw-r--r-- root/root 4804 2021-11-18 17:55 ./usr/share/doc/bwa-mem2/copyright drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/share/doc/bwa-mem2/examples/ -rw-r--r-- root/root 96 2021-11-18 17:55 ./usr/share/doc/bwa-mem2/examples/read1.fq -rw-r--r-- root/root 96 2021-11-18 17:55 ./usr/share/doc/bwa-mem2/examples/read2.fq -rw-r--r-- root/root 384 2021-11-18 17:55 ./usr/share/doc/bwa-mem2/examples/reads.fq -rw-r--r-- root/root 192 2021-11-18 17:55 ./usr/share/doc/bwa-mem2/examples/ref.fa drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/share/man/ drwxr-xr-x root/root 0 2025-04-17 09:11 ./usr/share/man/man1/ -rw-r--r-- root/root 1654 2025-04-17 09:11 ./usr/share/man/man1/bwa-mem2-mem.1.gz -rw-r--r-- root/root 360 2025-04-17 09:11 ./usr/share/man/man1/bwa-mem2.1.gz +------------------------------------------------------------------------------+ | Post Build Tue, 02 Sep 2025 19:29:23 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Tue, 02 Sep 2025 19:29:23 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Tue, 02 Sep 2025 19:29:25 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 25664 Build-Time: 119 Distribution: unstable Host Architecture: amd64 Install-Time: 3 Job: /srv/rebuilderd/tmp/rebuilderdS6PC0H/inputs/bwa-mem2_2.2.1-1.dsc Machine Architecture: amd64 Package: bwa-mem2 Package-Time: 132 Source-Version: 2.2.1-1 Space: 25664 Status: successful Version: 2.2.1-1+b1 -------------------------------------------------------------------------------- Finished at 2025-09-02T19:29:20Z Build needed 00:02:12, 25664k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderdS6PC0H/out checking bwa-mem2-dbgsym_2.2.1-1+b1_amd64.deb: size... sha256... sha1... md5... all OK checking bwa-mem2_2.2.1-1+b1_amd64.deb: size differs for bwa-mem2_2.2.1-1+b1_amd64.deb