Thu Apr 4 01:01:28 UTC 2024 I: starting to build bwa/experimental/i386 on jenkins on '2024-04-04 01:01' Thu Apr 4 01:01:28 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_4/13695/console.log Thu Apr 4 01:01:28 UTC 2024 I: Downloading source for experimental/bwa=0.7.17-8~0exp --2024-04-04 01:01:29-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/bwa/bwa_0.7.17-8%7e0exp.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2174 (2.1K) [text/prs.lines.tag] Saving to: ‘bwa_0.7.17-8~0exp.dsc’ 0K .. 100% 231M=0s 2024-04-04 01:01:29 (231 MB/s) - ‘bwa_0.7.17-8~0exp.dsc’ saved [2174/2174] Thu Apr 4 01:01:29 UTC 2024 I: bwa_0.7.17-8~0exp.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bwa Binary: bwa, libbwa-dev Architecture: any Version: 0.7.17-8~0exp Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Carlos Borroto , Ognyan Kulev , Michael R. Crusoe Homepage: http://bio-bwa.sourceforge.net/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/bwa Vcs-Git: https://salsa.debian.org/med-team/bwa.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, libsimde-dev (>= 0.7.3~0git20230118123246.d1e75cd) Package-List: bwa deb science optional arch=any libbwa-dev deb libdevel optional arch=any Checksums-Sha1: 77f9aac723110227ea51cb42011336d291d03723 232593 bwa_0.7.17.orig.tar.gz 2a212b75fa0dddfbf0e195cf9509a8ac6f45711e 10772 bwa_0.7.17-8~0exp.debian.tar.xz Checksums-Sha256: 980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd 232593 bwa_0.7.17.orig.tar.gz 87c1c7089ba725a7746723489304115a3d6c21b2eec26e7b843fbafd15006ebb 10772 bwa_0.7.17-8~0exp.debian.tar.xz Files: 63c54309e7dda2311d4658e18c7adffb 232593 bwa_0.7.17.orig.tar.gz d119308020ed937a00281d4aad897c68 10772 bwa_0.7.17-8~0exp.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmPNcXYACgkQPCZ2P2xn 5uKJ3hAAlhFrZC24Zeh6cJ47nyHegLxiF3HxrFtIlFtNnAt3URbAX6Y5T0XXtUcA QfSvLggLOdQiIC6SX5ZLaS3MUlGhdNq0cIpzSjPqMGq36p1vj/jQ1WkidCM3p107 i6ez2ACWYdvxez0rSs0LAtmj1RFF7aNMyPIw4parEIJo8rBZJqBEdxWcs8sRNhpu U1p7JZEIgtiogSLF26nzXbOgBMrBx5locDKiohz6AAhl7X7EtyB4ABoSYyJGeFIU eM+AWvxcGe/taozeiEIpKJYCndSmj2IRloMCieMamtxuJcUu+jFHQtcXi6/lG128 VQ5k5ncVdxj0Az6X+yO72HhYUhHsjkMLW8Pm+M2ThXK3Kt9ZL7e8zYDQpZxPM2Cb 6bz03OF3HSWgWN8do0TeiN0fiQGJSaasinEtZcZjAfUjftbAQFjuunPDra6+rfRb ScyyM33J6+tT9vUjcCKCVK3+2tFKldbfh6+GgGjjAZ20hKarjng45OtqVurKradt BcUGtbWb/ERXAQ2oMqM+NIkQWHPuDnwgkEnOZ3CEvRtmNtvi5wJtsSEIxd0qJyFb i2h6u+kxANvj6S65Yyhoctw+fbHwz8qKV6Zihp/W+C0xaKShgJNiuk4t3QnBEStf j4NohRpIXs1mDjYL4iavuW15ONzUGah+Yz7jiOpo2LjAoFGJo3s= =OO0N -----END PGP SIGNATURE----- Thu Apr 4 01:01:29 UTC 2024 I: Checking whether the package is not for us Thu Apr 4 01:01:29 UTC 2024 I: Starting 1st build on remote node ionos16-i386.debian.net. Thu Apr 4 01:01:29 UTC 2024 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Thu Apr 4 01:01:58 UTC 2024 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 6 19:24:30 -12 2025 I: pbuilder-time-stamp: 1746602670 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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: using eatmydata during job I: Copying source file I: copying [bwa_0.7.17-8~0exp.dsc] I: copying [./bwa_0.7.17.orig.tar.gz] I: copying [./bwa_0.7.17-8~0exp.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jan 22 17:25:10 2023 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bwa_0.7.17-8~0exp.dsc: no acceptable signature found dpkg-source: info: extracting bwa in bwa-0.7.17 dpkg-source: info: unpacking bwa_0.7.17.orig.tar.gz dpkg-source: info: unpacking bwa_0.7.17-8~0exp.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_heap_block_overrun dpkg-source: info: applying fix_build_on_freebsd.patch dpkg-source: info: applying CVE-2019-10269.patch dpkg-source: info: applying simde dpkg-source: info: applying spelling dpkg-source: info: applying gcc10.patch dpkg-source: info: applying hurd I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/83005/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='experimental' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='d72edbacdeae4bdb86f83f6b73ab591f' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='83005' 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.xjHEnWiW/pbuilderrc_vXlA --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xjHEnWiW/b1 --logfile b1/build.log bwa_0.7.17-8~0exp.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos16-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 29 13:56 /bin -> usr/bin I: user script /srv/workspace/pbuilder/83005/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: i386 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 (>= 0.7.3~0git20230118123246.d1e75cd) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19702 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 (>= 0.7.3~0git20230118123246.d1e75cd); however: Package libsimde-dev 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} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsimde-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{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, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 20.7 MB of archives. After unpacking 83.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-3+b1 [1195 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.39.3-11 [93.7 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 man-db i386 2.12.0-4 [1418 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.191-1 [194 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 libsimde-dev all 0.8.0-1 [458 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg-3.1 [915 kB] Fetched 20.7 MB in 1s (18.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19702 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_i386.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_i386.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-3+b1_i386.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.39.3-11_i386.deb ... Unpacking bsdextrautils (2.39.3-11) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.7-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.0-4_i386.deb ... Unpacking man-db (2.12.0-4) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../22-libelf1t64_0.191-1_i386.deb ... Unpacking libelf1t64:i386 (0.191-1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../24-libicu72_72.1-4+b1_i386.deb ... Unpacking libicu72:i386 (72.1-4+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b2_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_i386.deb ... Unpacking gettext (0.21-14+b1) ... 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_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../30-libsimde-dev_0.8.0-1_all.deb ... Unpacking libsimde-dev (0.8.0-1) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../31-zlib1g-dev_1%3a1.3.dfsg-3.1_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.3.dfsg-3.1) ... Setting up libpipeline1:i386 (1.5.7-2) ... Setting up libsimde-dev (0.8.0-1) ... Setting up libicu72:i386 (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-11) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:i386 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:i386 (0.191-1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-4) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.37-15.1) ... 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-0.7.17/ && 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_0.7.17-8~0exp_source.changes dpkg-buildpackage: info: source package bwa dpkg-buildpackage: info: source version 0.7.17-8~0exp dpkg-buildpackage: info: source distribution experimental dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_auto_clean make -j22 clean make[1]: Entering directory '/build/reproducible-path/bwa-0.7.17' rm -f gmon.out *.o a.out bwa *~ *.a make[1]: Leaving directory '/build/reproducible-path/bwa-0.7.17' 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-0.7.17' dh_auto_build -- CFLAGS="-Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now" DFLAGS="-DHAVE_PTHREAD" make -j22 "INSTALL=install --strip-program=true" "CFLAGS=-Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now" DFLAGS=-DHAVE_PTHREAD make[2]: Entering directory '/build/reproducible-path/bwa-0.7.17' gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD utils.c -o utils.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD kthread.c -o kthread.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD kstring.c -o kstring.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD ksw.c -o ksw.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwt.c -o bwt.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bntseq.c -o bntseq.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwa.c -o bwa.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwamem.c -o bwamem.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwamem_pair.c -o bwamem_pair.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwamem_extra.c -o bwamem_extra.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD malloc_wrap.c -o malloc_wrap.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD QSufSort.c -o QSufSort.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD rope.c -o rope.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD rle.c -o rle.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD is.c -o is.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtindex.c -o bwtindex.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwashm.c -o bwashm.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwase.c -o bwase.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtgap.c -o bwtgap.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtaln.c -o bwtaln.o bwt_gen.c: In function 'BWTIncBuildRelativeRank': bwt_gen.c:879:17: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable] 879 | bgint_t oldInverseSa0RelativeRank = 0; | ^~~~~~~~~~~~~~~~~~~~~~~~~ bwt_gen.c: In function 'BWTIncMergeBwt': bwt_gen.c:953:22: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable] 953 | unsigned int bitsInWordMinusBitPerChar; | ^~~~~~~~~~~~~~~~~~~~~~~~~ rope.c: In function 'rope_restore_node': rope.c:282:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 282 | fread(&is_bottom, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ rope.c:283:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 283 | fread(&n, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~~ rope.c:291:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 291 | fread(p[i].c, 8, 6, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ rope.c:292:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 292 | fread(q, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~ rope.c:293:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 293 | fread(q + 1, 1, *q, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ rope.c: In function 'rope_restore': bwashm.c: In function 'bwa_shm_stage': bwashm.c:33:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result] 33 | ftruncate(shmid, BWA_CTL_SIZE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rope.c:312:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 312 | fread(&r->max_nodes, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwashm.c:70:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | ftruncate(shmid, idx->l_mem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ rope.c:313:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 313 | fread(&r->block_len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bamlite.c -o bamlite.o bwamem_pair.c: In function 'mem_pestat': bwamem_pair.c:65:106: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); | ~~^ ~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d bwamem_pair.c:65:111: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); | ~~^ ~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d bwamem_pair.c:65:116: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); | ~~^ ~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d bwamem_pair.c:65:121: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 65 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n); | ~~^ ~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwape.c -o bwape.o bwamem.c: In function 'mem_align1_core': bwamem.c:1075:33: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1075 | err_printf("* %ld chains remain after removing duplicated chains\n", regs.n); | ~~^ ~~~~~~ | | | | long int size_t {aka unsigned int} | %d gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD kopen.c -o kopen.o ksw.c: In function 'ksw_u8': ksw.c:132:14: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 132 | zero = _mm_set1_epi32(0); | ^ gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD pemerge.c -o pemerge.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD maxk.c -o maxk.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD fastmap.c -o fastmap.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_pair.c -o bwtsw2_pair.o fastmap.c: In function 'main_fastmap': fastmap.c:413:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 413 | err_printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l); | ~~^ ~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD main.c -o main.o ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o ar: `u' modifier ignored since `D' is the default (see `U') gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt make[2]: Leaving directory '/build/reproducible-path/bwa-0.7.17' make[1]: Leaving directory '/build/reproducible-path/bwa-0.7.17' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/bwa-0.7.17' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/bwa-0.7.17' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/bwa-0.7.17' dh_installchangelogs NEWS.md make[1]: Leaving directory '/build/reproducible-path/bwa-0.7.17' dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/bwa-0.7.17' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.0-1), " dpkg-gencontrol: warning: package bwa: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bwa: substitution variable ${perl:Depends} unused, but is defined make[1]: Leaving directory '/build/reproducible-path/bwa-0.7.17' dh_md5sums dh_builddeb dpkg-deb: building package 'bwa' in '../bwa_0.7.17-8~0exp_i386.deb'. dpkg-deb: building package 'bwa-dbgsym' in '../bwa-dbgsym_0.7.17-8~0exp_i386.deb'. dpkg-deb: building package 'libbwa-dev' in '../libbwa-dev_0.7.17-8~0exp_i386.deb'. dpkg-genbuildinfo --build=binary -O../bwa_0.7.17-8~0exp_i386.buildinfo dpkg-genchanges --build=binary -O../bwa_0.7.17-8~0exp_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/83005 and its subdirectories I: Current time: Tue May 6 19:24:57 -12 2025 I: pbuilder-time-stamp: 1746602697 Thu Apr 4 01:01:59 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net. Thu Apr 4 01:01:59 UTC 2024 I: Preparing to do remote build '2' on ionos2-i386.debian.net. Thu Apr 4 01:03:09 UTC 2024 I: Deleting $TMPDIR on ionos2-i386.debian.net. Thu Apr 4 01:03:10 UTC 2024 I: bwa_0.7.17-8~0exp_i386.changes: Format: 1.8 Date: Sun, 22 Jan 2023 18:24:44 +0100 Source: bwa Binary: bwa bwa-dbgsym libbwa-dev Architecture: i386 Version: 0.7.17-8~0exp Distribution: experimental Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: bwa - Burrows-Wheeler Aligner libbwa-dev - Burrows-Wheeler Aligner source files Changes: bwa (0.7.17-8~0exp) experimental; urgency=medium . * Experimental rebuild with SIMDe 0.7.3~0git20230118123246.d1e75cd Checksums-Sha1: 73e92b78ed2a963230dec80579cce0eb6e3111db 417088 bwa-dbgsym_0.7.17-8~0exp_i386.deb 1a03ebff663dd2cb2521da0062a86a4fe16a5b2c 5427 bwa_0.7.17-8~0exp_i386.buildinfo bb979f09d7cebd07bb38ab536e5883f7da3c818b 235184 bwa_0.7.17-8~0exp_i386.deb 0a3e56d6bb385b9eb6570385101aafe86db266da 169696 libbwa-dev_0.7.17-8~0exp_i386.deb Checksums-Sha256: 39b33877d9860efe5404f2f400d73065d07b474ca6210ed55b284bfacf636707 417088 bwa-dbgsym_0.7.17-8~0exp_i386.deb 4ae46437084cd7c3e8dfb8451fe9bfd5c56edbe0b3658d29d68fdd05c5276898 5427 bwa_0.7.17-8~0exp_i386.buildinfo a178bca2da13b254af5c172ebde514ead10541c6363a76616623a28f640efd13 235184 bwa_0.7.17-8~0exp_i386.deb 437d8101024db5a352836f2d3d0536bbedda01c31c621c16bcfb91565aec8550 169696 libbwa-dev_0.7.17-8~0exp_i386.deb Files: fd75889ad3003ae0a2a7b8ffe1efc8d2 417088 debug optional bwa-dbgsym_0.7.17-8~0exp_i386.deb c0000d69f21f364fde2271176ea1a7a3 5427 science optional bwa_0.7.17-8~0exp_i386.buildinfo f5a8f05e27dd99214b29d5f935b47a9e 235184 science optional bwa_0.7.17-8~0exp_i386.deb dc25c7e102988be7538d799d7977cc9f 169696 libdevel optional libbwa-dev_0.7.17-8~0exp_i386.deb Thu Apr 4 01:03:11 UTC 2024 I: diffoscope 262 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_4-13695.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.xjHEnWiW/bwa_0.7.17-8~0exp.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.xjHEnWiW/bwa_0.7.17-8~0exp.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.xjHEnWiW/bwa_0.7.17-8~0exp.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.xjHEnWiW/b1/bwa_0.7.17-8~0exp_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.xjHEnWiW/b2/bwa_0.7.17-8~0exp_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.476s) 0.476s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.031s) 0.031s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 912ms CPU time consumed: 914ms Thu Apr 4 01:03:19 UTC 2024 I: diffoscope 262 found no differences in the changes files, and a .buildinfo file also exists. Thu Apr 4 01:03:19 UTC 2024 I: bwa from experimental built successfully and reproducibly on i386. Thu Apr 4 01:03:20 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Apr 4 01:03:20 UTC 2024 I: Submitting 8.0K b1/bwa_0.7.17-8~0exp_i386.buildinfo.asc Thu Apr 4 01:03:21 UTC 2024 I: Submitting 8.0K b2/bwa_0.7.17-8~0exp_i386.buildinfo.asc Thu Apr 4 01:03:23 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Apr 4 01:03:23 UTC 2024 I: Done submitting .buildinfo files. Thu Apr 4 01:03:23 UTC 2024 I: Removing signed bwa_0.7.17-8~0exp_i386.buildinfo.asc files: removed './b1/bwa_0.7.17-8~0exp_i386.buildinfo.asc' removed './b2/bwa_0.7.17-8~0exp_i386.buildinfo.asc'