I: pbuilder: network access will be disabled during build
I: Current time: Sat Apr 11 06:02:42 -12 2026
I: pbuilder-time-stamp: 1775930562
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 [grabix_0.1.7-5.dsc]
I: copying [./grabix_0.1.7.orig.tar.gz]
I: copying [./grabix_0.1.7-5.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./grabix_0.1.7-5.dsc: unsupported subcommand
dpkg-source: info: extracting grabix in grabix-0.1.7
dpkg-source: info: unpacking grabix_0.1.7.orig.tar.gz
dpkg-source: info: unpacking grabix_0.1.7-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_assignment_of_char_to_pointer.patch
dpkg-source: info: applying Hardening.patch
dpkg-source: info: applying warnings.patch
dpkg-source: info: applying introduceLTO.patch
dpkg-source: info: applying fix_test.patch
dpkg-source: info: applying 2to3.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/4123360/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='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='3809cb0be03a4ab69c2593ecbee023e2'
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='4123360'
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.8mRLrmWq/pbuilderrc_dlQT --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.8mRLrmWq/b1 --logfile b1/build.log grabix_0.1.7-5.dsc'
SUDO_GID='110'
SUDO_UID='105'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos5-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/4123360/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: amd64
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, python3, tabix, time, less
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19783 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on python3; however:
Package python3 is not installed.
pbuilder-satisfydepends-dummy depends on tabix; however:
Package tabix is not installed.
pbuilder-satisfydepends-dummy depends on time; however:
Package time is not installed.
pbuilder-satisfydepends-dummy depends on less; however:
Package less 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} less{a} libarchive-zip-perl{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libhtscodecs2{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tabix{a} time{a} tzdata{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 50 newly installed, 0 to remove and 0 not upgraded.
Need to get 28.8 MB of archives. After unpacking 108 MB will be used.
Writing extended state information...
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Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
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Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB]
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Get: 15 http://deb.debian.org/debian unstable/main amd64 less amd64 643-1 [148 kB]
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Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
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Get: 20 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-7 [294 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 37 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.21+ds-1 [496 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 time amd64 1.9-0.2 [50.8 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Fetched 28.8 MB in 3s (9045 kB/s)
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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
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Unpacking libhtscodecs2:amd64 (1.6.1-2) ...
Selecting previously unselected package tabix.
Preparing to unpack .../34-tabix_1.21+ds-1_amd64.deb ...
Unpacking tabix (1.21+ds-1) ...
Selecting previously unselected package time.
Preparing to unpack .../35-time_1.9-0.2_amd64.deb ...
Unpacking time (1.9-0.2) ...
Selecting previously unselected package zlib1g-dev:amd64.
Preparing to unpack .../36-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ...
Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libhtscodecs2:amd64 (1.6.1-2) ...
Setting up media-types (13.0.0) ...
Setting up libpipeline1:amd64 (1.5.8-1) ...
Setting up time (1.9-0.2) ...
Setting up libicu72:amd64 (72.1-6) ...
Setting up bsdextrautils (2.40.4-5) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.24.1) ...
Setting up libmagic1t64:amd64 (1:5.45-3+b1) ...
Setting up libdeflate0:amd64 (1.23-1+b1) ...
Setting up less (643-1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-7) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:amd64 (0.192-4) ...
Setting up tzdata (2025a-2) ...
Current default time zone: 'Etc/UTC'
Local time is now: Sat Apr 11 18:03:04 UTC 2026.
Universal Time is now: Sat Apr 11 18:03:04 UTC 2026.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up autotools-dev (20220109.1) ...
Setting up libunistring5:amd64 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libffi8:amd64 (3.4.7-1) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:amd64 (0.0.8-1+b2) ...
Setting up netbase (6.4) ...
Setting up tabix (1.21+ds-1) ...
Setting up readline-common (8.2-6) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libreadline8t64:amd64 (8.2-6) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ...
Setting up libpython3-stdlib:amd64 (3.13.2-2) ...
Setting up python3.13 (3.13.2-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up python3 (3.13.2-2) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.24.1) ...
Processing triggers for libc-bin (2.41-3) ...
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/grabix-0.1.7/ && 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 > ../grabix_0.1.7-5_source.changes
dpkg-buildpackage: info: source package grabix
dpkg-buildpackage: info: source version 0.1.7-5
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
dh_auto_clean
make -j42 clean
make[1]: Entering directory '/build/reproducible-path/grabix-0.1.7'
rm -f grabix
make[1]: Leaving directory '/build/reproducible-path/grabix-0.1.7'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j42 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/grabix-0.1.7'
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/grabix-0.1.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -flto -o grabix grabix_main.cpp grabix.cpp bgzf.c -Wl,-z,relro -Wl,-z,now -lstdc++ -lz -Wl,-flto
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++
make[1]: Leaving directory '/build/reproducible-path/grabix-0.1.7'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/grabix-0.1.7'
PATH=/build/reproducible-path/grabix-0.1.7:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games sh debian/testdata/test.sh
indexing
0.15user 0.00system 0:00.15elapsed 99%CPU (0avgtext+0avgdata 3628maxresident)k
0inputs+8outputs (0major+184minor)pagefaults 0swaps
indexed
checking indexing at bounds:
..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
PASS
OK ./debian/testdata/test.clinvar.vcf
OK ./debian/testdata/test.PLs.vcf
OK ./debian/testdata/test.exac.vcf
OK ./debian/testdata/test.fusions.vcf
OK ./debian/testdata/test.cosmic.vcf
rm -f test.cnt.gz test.cnt.gz.gbi
make[1]: Leaving directory '/build/reproducible-path/grabix-0.1.7'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/grabix/
dh_install
dh_installdocs
dh_installchangelogs
dh_installexamples
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'grabix-dbgsym' in '../grabix-dbgsym_0.1.7-5_amd64.deb'.
dpkg-deb: building package 'grabix' in '../grabix_0.1.7-5_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../grabix_0.1.7-5_amd64.buildinfo
dpkg-genchanges --build=binary -O../grabix_0.1.7-5_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/4123360 and its subdirectories
I: Current time: Sat Apr 11 06:03:28 -12 2026
I: pbuilder-time-stamp: 1775930608