Tue Oct 15 08:58:02 UTC 2024 I: starting to build bwa/trixie/armhf on jenkins on '2024-10-15 08:57' Tue Oct 15 08:58:02 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_33/16795/console.log Tue Oct 15 08:58:02 UTC 2024 I: Downloading source for trixie/bwa=0.7.18-1 --2024-10-15 08:58:02-- http://deb.debian.org/debian/pool/main/b/bwa/bwa_0.7.18-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2103 (2.1K) [text/prs.lines.tag] Saving to: ‘bwa_0.7.18-1.dsc’ 0K .. 100% 208M=0s 2024-10-15 08:58:02 (208 MB/s) - ‘bwa_0.7.18-1.dsc’ saved [2103/2103] Tue Oct 15 08:58:02 UTC 2024 I: bwa_0.7.18-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bwa Binary: bwa, libbwa-dev Architecture: any Version: 0.7.18-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Carlos Borroto , Ognyan Kulev , Michael R. Crusoe Homepage: https://bio-bwa.sourceforge.net/ Standards-Version: 4.6.2 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 Package-List: bwa deb science optional arch=any libbwa-dev deb libdevel optional arch=any Checksums-Sha1: a79dbcac2e085ac58beb137ed4917f71c8e0220c 238036 bwa_0.7.18.orig.tar.gz 8a543f0711dcb05a3964a0fa62e4ff586cdbfb7c 10056 bwa_0.7.18-1.debian.tar.xz Checksums-Sha256: 194788087f7b9a77c0114aa481b2ef21439f6abab72488c83917302e8d0e7870 238036 bwa_0.7.18.orig.tar.gz 4bd079669d2433711b20d303648923c4b96e0e68085574f220dc830ced8be171 10056 bwa_0.7.18-1.debian.tar.xz Files: f1c99c98f1c1cc7081f31394d95b0d87 238036 bwa_0.7.18.orig.tar.gz 11dd2c9dbde5a57d2203fda0f9aceb51 10056 bwa_0.7.18-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmbcP/MACgkQPCZ2P2xn 5uI5iRAAj5hHQBAuvKyQWVDYanHZoEzYFVsihFp4GScJzjrX/mhtzHRyApXUvrHh hQsYin3pZRIw0K3nJKj31gXztemrTVXQ2asM2VT++j7oUwAaOsA01ZdBwgkbl8M3 eHdln9kRU4HU2R4MtZHJkzMU3Re+VQuXsSZIWJAb55a3Dy6vbwHK9cBBOWtHZCiR UeXm7tDlYisXSIWqN+9UVmZdNekmwPXLTDLY4vq0CQzJQ5SzqUJImuTRE2rOZppE uwMBoGer3MXLh00e754Cc+6Qv+o4R/Jk0zlEfZ89k9H4hB69AuigRbg5ZO1dWAtA 8Gwp+Y+RccbASkOZcpxNqnrpgMmcboTkh8mOocLqVOrkdUfbROGr6tsTjvmq/ARc jTGsObikNMtWwWUZHlihK58SMCTOMSlmNKXavoGVrFepwyXhe5m6Wbdi1v5zOH0a oQtmlyLZBu+qnqPkB4zOKM7fjFT/jUerU51jFQawC51KUGvf9g1W3weJDotZdyU0 BZzDL5/c9uJXmFBmt2eEQVB5bpbqGGk93lqlKZSHH78nooMmwzfcyY1TSZZ+vs1O ReeCrC+j2BoBTl6d58C7rTqIhXZZkUJaRyfp3u/LQ9tOwSdce/x+jUsxfDWJI+6J 2g5wLk/O38jCi2uIpTWbpm5QbQWh186gia+hs7bGQQNTeGYUKH4= =lEdE -----END PGP SIGNATURE----- Tue Oct 15 08:58:02 UTC 2024 I: Checking whether the package is not for us Tue Oct 15 08:58:02 UTC 2024 I: Starting 1st build on remote node virt32z-armhf-rb.debian.net. Tue Oct 15 08:58:02 UTC 2024 I: Preparing to do remote build '1' on virt32z-armhf-rb.debian.net. Tue Oct 15 08:59:24 UTC 2024 I: Deleting $TMPDIR on virt32z-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Oct 14 20:58:08 -12 2024 I: pbuilder-time-stamp: 1728982688 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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_0.7.18-1.dsc] I: copying [./bwa_0.7.18.orig.tar.gz] I: copying [./bwa_0.7.18-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Sep 7 11:58:43 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bwa_0.7.18-1.dsc: no acceptable signature found dpkg-source: info: extracting bwa in bwa-0.7.18 dpkg-source: info: unpacking bwa_0.7.18.orig.tar.gz dpkg-source: info: unpacking bwa_0.7.18-1.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 spelling dpkg-source: info: applying hurd I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/17314/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='3cdf6c5567f64679a2216109989a57df' 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='17314' 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.UEYsyP76/pbuilderrc_Ebe2 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UEYsyP76/b1 --logfile b1/build.log bwa_0.7.18-1.dsc' SUDO_GID='110' SUDO_UID='103' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32z 6.1.0-26-armmp-lpae #1 SMP Debian 6.1.112-1 (2024-09-30) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/17314/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: armhf 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 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19508 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. 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} 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, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 20.0 MB of archives. After unpacking 71.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.2-9 [88.8 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-2 [183 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-5 [9075 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.1 [604 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1 [904 kB] Fetched 20.0 MB in 0s (43.9 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 ... 19508 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_armhf.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_armhf.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_armhf.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-9_armhf.deb ... Unpacking bsdextrautils (2.40.2-9) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... 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_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... 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 libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../21-libelf1t64_0.191-2_armhf.deb ... Unpacking libelf1t64:armhf (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../23-libicu72_72.1-5_armhf.deb ... Unpacking libicu72:armhf (72.1-5) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_armhf.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-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 .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../29-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libicu72:armhf (72.1-5) ... Setting up bsdextrautils (2.40.2-9) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:armhf (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:armhf (0.191-2) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.1) ... 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 (1.14.0-1) ... Setting up gettext (0.22.5-2) ... 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 (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... 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 (13.20) ... Processing triggers for libc-bin (2.40-3) ... 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-0.7.18/ && 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_0.7.18-1_source.changes dpkg-buildpackage: info: source package bwa dpkg-buildpackage: info: source version 0.7.18-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_auto_clean make -j3 clean make[1]: Entering directory '/build/reproducible-path/bwa-0.7.18' rm -f gmon.out *.o a.out bwa *~ *.a make[1]: Leaving directory '/build/reproducible-path/bwa-0.7.18' 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-0.7.18' dh_auto_build -- CFLAGS="-Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now" DFLAGS="-DHAVE_PTHREAD" make -j3 "INSTALL=install --strip-program=true" "CFLAGS=-Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now" DFLAGS=-DHAVE_PTHREAD make[2]: Entering directory '/build/reproducible-path/bwa-0.7.18' gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 utils.c -o utils.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 kthread.c -o kthread.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 kstring.c -o kstring.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 ksw.c -o ksw.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwt.c -o bwt.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bntseq.c -o bntseq.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwa.c -o bwa.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwamem.c -o bwamem.o bwamem.c: In function 'mem_align1_core': bwamem.c:1105:33: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1105 | 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-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwamem_pair.c -o bwamem_pair.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwamem_extra.c -o bwamem_extra.o bwamem_pair.c: In function 'mem_pestat': bwamem_pair.c:91:106: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 91 | 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:91:111: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 91 | 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:91:116: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 91 | 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:91:121: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 91 | 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-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 malloc_wrap.c -o malloc_wrap.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 QSufSort.c -o QSufSort.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwt_gen.c -o bwt_gen.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; | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 rope.c -o rope.o 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': 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 rle.c -o rle.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 is.c -o is.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwtindex.c -o bwtindex.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwashm.c -o bwashm.o 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwashm.c:70:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | ftruncate(shmid, idx->l_mem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwase.c -o bwase.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwaseqio.c -o bwaseqio.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwtgap.c -o bwtgap.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwtaln.c -o bwtaln.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bamlite.c -o bamlite.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwape.c -o bwape.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 kopen.c -o kopen.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 pemerge.c -o pemerge.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 maxk.c -o maxk.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwtsw2_core.c -o bwtsw2_core.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwtsw2_main.c -o bwtsw2_main.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwtsw2_aux.c -o bwtsw2_aux.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwt_lite.c -o bwt_lite.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwtsw2_chain.c -o bwtsw2_chain.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 fastmap.c -o fastmap.o fastmap.c: In function 'main_fastmap': fastmap.c:448:39: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 448 | 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-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bwtsw2_pair.c -o bwtsw2_pair.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 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-0.7.18=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now 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-0.7.18' make[1]: Leaving directory '/build/reproducible-path/bwa-0.7.18' 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-0.7.18' 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-0.7.18' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/bwa-0.7.18' dh_installchangelogs NEWS.md make[1]: Leaving directory '/build/reproducible-path/bwa-0.7.18' 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/bwa-0.7.18' dpkg-query: no packages found matching libsimde-dev dh_gencontrol -- -Vsimde:Built-Using="" 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-0.7.18' dh_md5sums dh_builddeb dpkg-deb: building package 'bwa' in '../bwa_0.7.18-1_armhf.deb'. dpkg-deb: building package 'bwa-dbgsym' in '../bwa-dbgsym_0.7.18-1_armhf.deb'. dpkg-deb: building package 'libbwa-dev' in '../libbwa-dev_0.7.18-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../bwa_0.7.18-1_armhf.buildinfo dpkg-genchanges --build=binary -O../bwa_0.7.18-1_armhf.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: including full 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/17314 and its subdirectories I: Current time: Mon Oct 14 20:59:15 -12 2024 I: pbuilder-time-stamp: 1728982755 Tue Oct 15 08:59:27 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt64c-armhf-rb.debian.net. Tue Oct 15 08:59:27 UTC 2024 I: Preparing to do remote build '2' on virt64c-armhf-rb.debian.net. Tue Oct 15 09:01:05 UTC 2024 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net. Tue Oct 15 09:01:08 UTC 2024 I: bwa_0.7.18-1_armhf.changes: Format: 1.8 Date: Sat, 07 Sep 2024 13:58:12 +0200 Source: bwa Binary: bwa bwa-dbgsym libbwa-dev Architecture: armhf Version: 0.7.18-1 Distribution: unstable 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 (0.7.18-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.2 (routine-update) Use secure URI in Homepage field. * Removed 2 patches applied upstream (CVE-2019-10269, gcc10). Removed no-longer-needed SIMDe patch. Checksums-Sha1: dc3d88e63e86d1a867fc6de72ba29defbb38b49a 452636 bwa-dbgsym_0.7.18-1_armhf.deb fa720634914a00147ef515ad72852257fa1292b8 5016 bwa_0.7.18-1_armhf.buildinfo f8b4caa38dc17a3ce05811b5ec64c7c2a9867fda 197996 bwa_0.7.18-1_armhf.deb eba8e4d0f1c43d1e2fa598c1286ba6bb75b72268 150972 libbwa-dev_0.7.18-1_armhf.deb Checksums-Sha256: 064517f803776350fb59d925e40cca47b2ac68263be7b5b98730a9c125f4224e 452636 bwa-dbgsym_0.7.18-1_armhf.deb 6e2447dffec8f60e670fe4a9d0be6f08175b80b6e877c3025685493c6c1e276b 5016 bwa_0.7.18-1_armhf.buildinfo 39134773a7203f2c35dbf703506759740fdf7790ec005262910afca8ff66e967 197996 bwa_0.7.18-1_armhf.deb ff6e8ff2aff8f79e1575adc6a3005f9be2565b36b52a0927aef591de9b003c1a 150972 libbwa-dev_0.7.18-1_armhf.deb Files: ed2b0ac8081c18043de8554fb225a992 452636 debug optional bwa-dbgsym_0.7.18-1_armhf.deb 492e94df3cd9978fffefbc792ab50f7c 5016 science optional bwa_0.7.18-1_armhf.buildinfo fc4268a3c495a7b20ee83c0deb0688e4 197996 science optional bwa_0.7.18-1_armhf.deb 6760d0d1e7c1598b99bcfceb1c1745b0 150972 libdevel optional libbwa-dev_0.7.18-1_armhf.deb Tue Oct 15 09:01:09 UTC 2024 I: diffoscope 280 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_33-16795.service Warning: program compiled against libxml 212 using older 209 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.UEYsyP76/bwa_0.7.18-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.UEYsyP76/bwa_0.7.18-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.UEYsyP76/bwa_0.7.18-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.UEYsyP76/b1/bwa_0.7.18-1_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.UEYsyP76/b2/bwa_0.7.18-1_armhf.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: 0.422s) 0.422s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.027s) 0.027s 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: 776ms CPU time consumed: 773ms Tue Oct 15 09:01:10 UTC 2024 I: diffoscope 280 found no differences in the changes files, and a .buildinfo file also exists. Tue Oct 15 09:01:10 UTC 2024 I: bwa from trixie built successfully and reproducibly on armhf. Tue Oct 15 09:01:12 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Oct 15 09:01:12 UTC 2024 I: Submitting 8.0K b1/bwa_0.7.18-1_armhf.buildinfo.asc Tue Oct 15 09:01:13 UTC 2024 I: Submitting 8.0K b2/bwa_0.7.18-1_armhf.buildinfo.asc Tue Oct 15 09:01:13 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Oct 15 09:01:13 UTC 2024 I: Done submitting .buildinfo files. Tue Oct 15 09:01:13 UTC 2024 I: Removing signed bwa_0.7.18-1_armhf.buildinfo.asc files: removed './b1/bwa_0.7.18-1_armhf.buildinfo.asc' removed './b2/bwa_0.7.18-1_armhf.buildinfo.asc'