Mon Oct 14 23:42:23 UTC 2024 I: starting to build bwa/unstable/armhf on jenkins on '2024-10-14 23:42'
Mon Oct 14 23:42:23 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_8/10457/console.log
Mon Oct 14 23:42:23 UTC 2024 I: Downloading source for unstable/bwa=0.7.18-1
--2024-10-14 23:42:23-- 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’
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2024-10-14 23:42:23 (284 MB/s) - ‘bwa_0.7.18-1.dsc’ saved [2103/2103]
Mon Oct 14 23:42:23 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 <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>, Andreas Tille <tille@debian.org>, Carlos Borroto <carlos.borroto@gmail.com>, Ognyan Kulev <ogi@debian.org>, Michael R. Crusoe <crusoe@debian.org>
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:
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8a543f0711dcb05a3964a0fa62e4ff586cdbfb7c 10056 bwa_0.7.18-1.debian.tar.xz
Checksums-Sha256:
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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
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Mon Oct 14 23:42:23 UTC 2024 I: Checking whether the package is not for us
Mon Oct 14 23:42:23 UTC 2024 I: Starting 1st build on remote node virt64a-armhf-rb.debian.net.
Mon Oct 14 23:42:23 UTC 2024 I: Preparing to do remote build '1' on virt64a-armhf-rb.debian.net.
Mon Oct 14 23:44:07 UTC 2024 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Mon Oct 14 11:42:29 -12 2024
I: pbuilder-time-stamp: 1728949349
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [bwa_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/21809/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='unstable'
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='a2d77a4788b54620b15c4e88d6057567'
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='21809'
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.zslrVo1c/pbuilderrc_iEOT --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zslrVo1c/b1 --logfile b1/build.log bwa_0.7.18-1.dsc'
SUDO_GID='114'
SUDO_UID='108'
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 virt64a 6.1.0-26-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/21809/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 <pbuilder-maint@lists.alioth.debian.org>
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 ... 21597 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 unstable/main armhf sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB]
Get: 3 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB]
Get: 4 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3 [42.0 kB]
Get: 5 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB]
Get: 6 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB]
Get: 7 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-5 [1091 kB]
Get: 8 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-9 [88.8 kB]
Get: 9 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB]
Get: 11 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB]
Get: 12 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB]
Get: 16 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB]
Get: 17 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-7 [517 kB]
Get: 18 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 21 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 22 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.191-2 [183 kB]
Get: 23 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB]
Get: 24 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5 [9075 kB]
Get: 25 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.1 [604 kB]
Get: 26 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB]
Get: 27 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 28 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 29 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB]
Get: 30 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1 [904 kB]
Fetched 20.0 MB in 0s (43.7 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
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(Reading database ... 100%
(Reading database ... 21597 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.
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Unpacking debhelper (13.20) ...
Selecting previously unselected package zlib1g-dev:armhf.
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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 <crusoe@debian.org>
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
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 bwamem_extra.c -o bwamem_extra.o
gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bwa-0.7.18=. -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/21809 and its subdirectories
I: Current time: Mon Oct 14 11:43:57 -12 2024
I: pbuilder-time-stamp: 1728949437
Mon Oct 14 23:44:10 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt32c-armhf-rb.debian.net.
Mon Oct 14 23:44:10 UTC 2024 I: Preparing to do remote build '2' on virt32c-armhf-rb.debian.net.
Mon Oct 14 23:45:31 UTC 2024 I: Deleting $TMPDIR on virt32c-armhf-rb.debian.net.
Mon Oct 14 23:45:33 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 <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <crusoe@debian.org>
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
101909607053bd2731ff1a316a79217f20105bd1 4999 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
20b40e71a65e8f9f3c17e437a4117be02765a33d1705632bf5a2b39e510e918b 4999 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
34f47e169c16af76a7bfe7e5e6d62f72 4999 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
Mon Oct 14 23:45:35 UTC 2024 I: diffoscope 280 will be used to compare the two builds:
Running as unit: rb-diffoscope-armhf_8-10457.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.zslrVo1c/bwa_0.7.18-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.zslrVo1c/bwa_0.7.18-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.zslrVo1c/bwa_0.7.18-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.zslrVo1c/b1/bwa_0.7.18-1_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.zslrVo1c/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: 0.390s)
0.390s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.025s)
0.025s 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: 1.058s
CPU time consumed: 777ms
Tue Oct 15 00:42:02 UTC 2024 I: diffoscope 280 found no differences in the changes files, and a .buildinfo file also exists.
Tue Oct 15 00:42:02 UTC 2024 I: bwa from unstable built successfully and reproducibly on armhf.
Tue Oct 15 00:42:07 UTC 2024 I: Submitting .buildinfo files to external archives:
Tue Oct 15 00:42:07 UTC 2024 I: Submitting 8.0K b1/bwa_0.7.18-1_armhf.buildinfo.asc
Tue Oct 15 00:42:35 UTC 2024 I: Submitting 8.0K b2/bwa_0.7.18-1_armhf.buildinfo.asc
Tue Oct 15 00:43:05 UTC 2024 E: Could not submit buildinfo from b2 to http://buildinfo.debian.net/api/submit
Tue Oct 15 00:43:05 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Tue Oct 15 00:43:05 UTC 2024 I: Done submitting .buildinfo files.
Tue Oct 15 00:43:05 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'