Fri Apr 18 11:02:31 UTC 2025 I: starting to build bwa-mem2/unstable/arm64 on jenkins on '2025-04-18 11:02' Fri Apr 18 11:02:31 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_10/66947/console.log Fri Apr 18 11:02:31 UTC 2025 I: Downloading source for unstable/bwa-mem2=2.2.1-1 --2025-04-18 11:02:32-- http://deb.debian.org/debian/pool/main/b/bwa-mem2/bwa-mem2_2.2.1-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2014 (2.0K) [text/prs.lines.tag] Saving to: ‘bwa-mem2_2.2.1-1.dsc’ 0K . 100% 261M=0s 2025-04-18 11:02:32 (261 MB/s) - ‘bwa-mem2_2.2.1-1.dsc’ saved [2014/2014] Fri Apr 18 11:02:32 UTC 2025 I: bwa-mem2_2.2.1-1.dsc -----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----- Fri Apr 18 11:02:32 UTC 2025 I: Checking whether the package is not for us Fri Apr 18 11:02:32 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Fri Apr 18 11:02:32 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Fri Apr 18 11:03:01 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Apr 17 23:02:34 -12 2025 I: pbuilder-time-stamp: 1744974154 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bwa-mem2_2.2.1-1.dsc] I: copying [./bwa-mem2_2.2.1.orig.tar.xz] I: copying [./bwa-mem2_2.2.1-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./bwa-mem2_2.2.1-1.dsc: unsupported subcommand dpkg-source: info: extracting bwa-mem2 in 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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1726561/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='aeda41e271534d1499a82e2ac506c7c1' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1726561' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.teOWsN4o/pbuilderrc_ZWk5 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.teOWsN4o/b1 --logfile b1/build.log bwa-mem2_2.2.1-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1726561/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libsimde-dev, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19954 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsimde-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 12.5 MB of archives. After unpacking 55.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-7 [285 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-3 [467 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Fetched 12.5 MB in 0s (81.2 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19954 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.41-4_arm64.deb ... Unpacking bsdextrautils (2.41-4) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../09-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-7_arm64.deb ... Unpacking m4 (1.4.19-7) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../24-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.4_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package help2man. Preparing to unpack .../30-help2man_1.49.3+b1_arm64.deb ... Unpacking help2man (1.49.3+b1) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../31-libsimde-dev_0.8.2-3_all.deb ... Unpacking libsimde-dev (0.8.2-3) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../32-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-3) ... Setting up bsdextrautils (2.41-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-7) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/bwa-mem2-2.2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bwa-mem2_2.2.1-1_source.changes dpkg-buildpackage: info: source package bwa-mem2 dpkg-buildpackage: info: source version 2.2.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 -j12 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 dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/bwa-mem2-2.2.1' dh_auto_build -- ARCH_FLAGS=' ' make -j12 "INSTALL=install --strip-program=true" "ARCH_FLAGS= " 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -g -O3 -fpermissive -g -O3 -fpermissive -Wdate-time -D_FORTIFY_SOURCE=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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -g -O3 -fpermissive -g -O3 -fpermissive -Wdate-time -D_FORTIFY_SOURCE=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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -g -O3 -fpermissive -g -O3 -fpermissive -Wdate-time -D_FORTIFY_SOURCE=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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -g -O3 -fpermissive -g -O3 -fpermissive -Wdate-time -D_FORTIFY_SOURCE=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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -g -O3 -fpermissive -g -O3 -fpermissive -Wdate-time -D_FORTIFY_SOURCE=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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -g -O3 -fpermissive -g -O3 -fpermissive -Wdate-time -D_FORTIFY_SOURCE=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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -g -O3 -fpermissive -g -O3 -fpermissive -Wdate-time -D_FORTIFY_SOURCE=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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -g -O3 -fpermissive -g -O3 -fpermissive -Wdate-time -D_FORTIFY_SOURCE=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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -g -O3 -fpermissive -g -O3 -fpermissive -Wdate-time -D_FORTIFY_SOURCE=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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -g -O3 -fpermissive -g -O3 -fpermissive -Wdate-time -D_FORTIFY_SOURCE=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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -g -O3 -fpermissive -g -O3 -fpermissive -Wdate-time -D_FORTIFY_SOURCE=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 src/bwamem.cpp:32:10: fatal error: immintrin.h: No such file or directory 32 | #include // For __rdtsc | ^~~~~~~~~~~~~ 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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -g -O3 -fpermissive -g -O3 -fpermissive -Wdate-time -D_FORTIFY_SOURCE=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 compilation terminated. make[3]: *** [Makefile:99: src/bwamem.o] Error 1 make[3]: *** Waiting for unfinished jobs.... 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/fastmap.cpp:40:10: fatal error: immintrin.h: No such file or directory 40 | #include // For __rdtsc | ^~~~~~~~~~~~~ compilation terminated. 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) | ^~~~~~~~~~ make[3]: *** [Makefile:99: src/fastmap.o] Error 1 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) | ^~~~~~~~~~ src/FMI_search.cpp:33:10: fatal error: immintrin.h: No such file or directory 33 | #include // For __rdtsc | ^~~~~~~~~~~~~ compilation terminated. make[3]: *** [Makefile:99: src/FMI_search.o] Error 1 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__); | ^~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' make[2]: *** [Makefile:105: multi] Error 2 make[2]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' dh_auto_build: error: make -j12 "INSTALL=install --strip-program=true" "ARCH_FLAGS= " returned exit code 2 make[1]: *** [debian/rules:20: override_dh_auto_build] Error 25 make[1]: Leaving directory '/build/reproducible-path/bwa-mem2-2.2.1' make: *** [debian/rules:13: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1726561 and its subdirectories Fri Apr 18 11:03:02 UTC 2025 W: No second build log, what happened?