Sun Jan 19 10:43:18 UTC 2025 I: starting to build chip-seq/trixie/arm64 on jenkins on '2025-01-19 10:43'
Sun Jan 19 10:43:18 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_5/78894/console.log
Sun Jan 19 10:43:18 UTC 2025 I: Downloading source for trixie/chip-seq=1.5.5-3
--2025-01-19 10:43:18-- http://deb.debian.org/debian/pool/main/c/chip-seq/chip-seq_1.5.5-3.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2020 (2.0K) [text/prs.lines.tag]
Saving to: ‘chip-seq_1.5.5-3.dsc’
0K . 100% 341M=0s
2025-01-19 10:43:18 (341 MB/s) - ‘chip-seq_1.5.5-3.dsc’ saved [2020/2020]
Sun Jan 19 10:43:18 UTC 2025 I: chip-seq_1.5.5-3.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: chip-seq
Binary: chip-seq, chip-seq-data
Architecture: any all
Version: 1.5.5-3
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://ccg.epfl.ch//chipseq
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/chip-seq
Vcs-Git: https://salsa.debian.org/med-team/chip-seq.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 12)
Package-List:
chip-seq deb science optional arch=any
chip-seq-data deb science optional arch=all
Checksums-Sha1:
c1d0fe6c413dbfcfc248a9ed2f49838a4b1384ac 5257567 chip-seq_1.5.5.orig.tar.gz
08d2558d0740ecc3cf754e4effad0821503c13fc 8840 chip-seq_1.5.5-3.debian.tar.xz
Checksums-Sha256:
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654d5dadedc5c1fa9e46f65a6ffdc1fa1571715e80f4c1b6e5908a63047e20b1 8840 chip-seq_1.5.5-3.debian.tar.xz
Files:
4e08c0558e2304415c766fa0bd3cbebd 5257567 chip-seq_1.5.5.orig.tar.gz
1c60740cc4de88131a34ce223804e7d5 8840 chip-seq_1.5.5-3.debian.tar.xz
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Sun Jan 19 10:43:18 UTC 2025 I: Checking whether the package is not for us
Sun Jan 19 10:43:18 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net.
Sun Jan 19 10:43:18 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net.
Sun Jan 19 10:44:24 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sat Feb 21 05:06:20 -12 2026
I: pbuilder-time-stamp: 1771693580
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 [chip-seq_1.5.5-3.dsc]
I: copying [./chip-seq_1.5.5.orig.tar.gz]
I: copying [./chip-seq_1.5.5-3.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./chip-seq_1.5.5-3.dsc: unsupported subcommand
dpkg-source: info: extracting chip-seq in chip-seq-1.5.5
dpkg-source: info: unpacking chip-seq_1.5.5.orig.tar.gz
dpkg-source: info: unpacking chip-seq_1.5.5-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_makefile.patch
dpkg-source: info: applying data_location.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/2185971/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='arm64'
IFS='
'
INVOCATION_ID='e7dc503cc4fb4aeaa65c749156f31e65'
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='2185971'
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.ErUfD9wI/pbuilderrc_I6M6 --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.ErUfD9wI/b1 --logfile b1/build.log chip-seq_1.5.5-3.dsc'
SUDO_GID='109'
SUDO_UID='104'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.4:3128'
I: uname -a
Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/2185971/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: arm64
Maintainer: Debian Pbuilder Team <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 (= 12)
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19969 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 (= 12); however:
Package debhelper-compat 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} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{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 19.9 MB of archives. After unpacking 79.9 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-4 [198 kB]
Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB]
Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB]
Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-4 [723 kB]
Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.23 [90.6 kB]
Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-2 [539 kB]
Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 24 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB]
Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-4 [1532 kB]
Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB]
Fetched 19.9 MB in 0s (120 MB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
(Reading database ...
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(Reading database ... 19969 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+b1_arm64.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:arm64.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ...
Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ...
Unpacking file (1:5.45-3+b1) ...
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Preparing to unpack .../04-gettext-base_0.22.5-4_arm64.deb ...
Unpacking gettext-base (0.22.5-4) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.23.0-7_arm64.deb ...
Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.40.4-1_arm64.deb ...
Unpacking bsdextrautils (2.40.4-1) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.8-1) ...
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Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ...
Unpacking man-db (2.13.0-1) ...
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Preparing to unpack .../10-m4_1.4.19-5_arm64.deb ...
Unpacking m4 (1.4.19-5) ...
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Unpacking autoconf (2.72-3) ...
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Unpacking autotools-dev (20220109.1) ...
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Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
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Unpacking libtool (2.5.4-2) ...
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Unpacking dh-autoreconf (20) ...
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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 ...
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Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package libunistring5:arm64.
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Unpacking libunistring5:arm64 (1.3-1) ...
Selecting previously unselected package libicu72:arm64.
Preparing to unpack .../24-libicu72_72.1-6_arm64.deb ...
Unpacking libicu72:arm64 (72.1-6) ...
Selecting previously unselected package libxml2:arm64.
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Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
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Unpacking gettext (0.22.5-4) ...
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Unpacking debhelper (13.23) ...
Setting up libpipeline1:arm64 (1.5.8-1) ...
Setting up libicu72:arm64 (72.1-6) ...
Setting up bsdextrautils (2.40.4-1) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.23) ...
Setting up libmagic1t64:arm64 (1:5.45-3+b1) ...
Setting up gettext-base (0.22.5-4) ...
Setting up m4 (1.4.19-5) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:arm64 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libunistring5:arm64 (1.3-1) ...
Setting up autopoint (0.22.5-4) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:arm64 (0.0.8-1+b2) ...
Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
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 (0.22.5-4) ...
Setting up libtool (2.5.4-2) ...
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 (1.23.0-7) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.23) ...
Processing triggers for libc-bin (2.40-5) ...
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/chip-seq-1.5.5/ && 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 > ../chip-seq_1.5.5-3_source.changes
dpkg-buildpackage: info: source package chip-seq
dpkg-buildpackage: info: source version 1.5.5-3
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 arm64
debian/rules clean
dh clean
dh_auto_clean
make -j12 clean
make[1]: Entering directory '/build/reproducible-path/chip-seq-1.5.5'
rm -rf chipcor chipextract chippart chippeak chipcenter chipscore tools/compactsga tools/countsga tools/featreplace tools/filter_counts tools/bed2sga tools/bed2bed_display tools/sga2bed tools/sga2wig *.o *~
make[1]: Leaving directory '/build/reproducible-path/chip-seq-1.5.5'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j12 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/chip-seq-1.5.5'
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/chip-seq-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=gnu99 -W -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -o chipcor chipcor.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/chip-seq-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=gnu99 -W -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -o chipextract chipextract.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/chip-seq-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=gnu99 -W -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -o chippart chippart.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/chip-seq-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=gnu99 -W -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/chip-seq-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=gnu99 -W -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -o chipscore chipscore.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/chip-seq-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=gnu99 -W -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -o tools/compactsga tools/compactsga.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/chip-seq-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=gnu99 -W -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -o tools/countsga tools/countsga.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/chip-seq-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=gnu99 -W -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -o tools/featreplace tools/featreplace.c
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/chip-seq-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=gnu99 -W -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -o tools/filter_counts tools/filter_counts.c
hashtable.c: In function 'MurmurHash3_x86_32':
hashtable.c:539:14: warning: this statement may fall through [-Wimplicit-fallthrough=]
539 | case 3: k1 ^= tail[2] << 16;
| ~~~^~~~~~~~~~~~~~~~
hashtable.c:540:3: note: here
540 | case 2: k1 ^= tail[1] << 8;
| ^~~~
hashtable.c:540:14: warning: this statement may fall through [-Wimplicit-fallthrough=]
540 | case 2: k1 ^= tail[1] << 8;
| ~~~^~~~~~~~~~~~~~~
hashtable.c:541:3: note: here
541 | case 1: k1 ^= tail[0];
| ^~~~
gcc -Wl,-z,relro -O3 -std=gnu99 -fPIC -lm -o chippeak chippeak.c hashtable.o
gcc -Wl,-z,relro -O3 -std=gnu99 -fPIC -lm -o chipcenter chipcenter.c hashtable.o
gcc -o tools/bed2sga tools/bed2sga.c hashtable.o -Wl,-z,relro -O3 -std=gnu99 -fPIC -lm
gcc -o tools/bed2bed_display tools/bed2bed_display.c hashtable.o -Wl,-z,relro -O3 -std=gnu99 -fPIC -lm
gcc -o tools/sga2bed tools/sga2bed.c hashtable.o -Wl,-z,relro -O3 -std=gnu99 -fPIC -lm
gcc -o tools/sga2wig tools/sga2wig.c hashtable.o -Wl,-z,relro -O3 -std=gnu99 -fPIC -lm
tools/bed2bed_display.c: In function 'main':
tools/bed2bed_display.c:564:7: warning: '__builtin_memcpy' writing 6 bytes into a region of size 5 [-Wstringop-overflow=]
564 | strcpy(options.visibility, "dense");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tools/bed2bed_display.c:557:31: note: destination object of size 5 allocated by 'malloc'
557 | if ((options.visibility = malloc(5 * sizeof(char))) == NULL) {
| ^~~~~~~~~~~~~~~~~~~~~~~~
make[1]: Leaving directory '/build/reproducible-path/chip-seq-1.5.5'
dh_auto_test
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
make -j12 install DESTDIR=/build/reproducible-path/chip-seq-1.5.5/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/chip-seq-1.5.5'
mkdir -p /build/reproducible-path/chip-seq-1.5.5/debian/tmp/usr/bin
mv chipcor chipextract chippart chippeak chipcenter chipscore tools/compactsga tools/countsga tools/featreplace tools/filter_counts tools/bed2sga tools/bed2bed_display tools/sga2bed tools/sga2wig /build/reproducible-path/chip-seq-1.5.5/debian/tmp/usr/bin
cp -p tools/check_bed.pl tools/chr_replace_sga.pl tools/eland2sga.pl tools/fps2sga.pl tools/gff2sga.pl tools/partit2bed.pl tools/partit2gff.pl tools/sga2fps.pl tools/sga2gff.pl /build/reproducible-path/chip-seq-1.5.5/debian/tmp/usr/bin
make[1]: Leaving directory '/build/reproducible-path/chip-seq-1.5.5'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/chip-seq-1.5.5'
dh_install
for perlscript in `grep -lR '#!/usr/local/bin/perl' debian/*/usr` ; do \
sed -i '1s+#!/usr/local/bin/perl+#!/usr/bin/perl+' ${perlscript} ; \
done
make[1]: Leaving directory '/build/reproducible-path/chip-seq-1.5.5'
dh_installdocs
dh_installchangelogs
dh_installexamples
debian/rules override_dh_installman
make[1]: Entering directory '/build/reproducible-path/chip-seq-1.5.5'
dh_installman --language=C
make[1]: Leaving directory '/build/reproducible-path/chip-seq-1.5.5'
dh_lintian
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
debian/rules override_dh_fixperms-indep
make[1]: Entering directory '/build/reproducible-path/chip-seq-1.5.5'
dh_fixperms -i
find debian/chip-seq-data/usr/share/chip-seq/ -type f -exec chmod -x \{\} \;
make[1]: Leaving directory '/build/reproducible-path/chip-seq-1.5.5'
dh_fixperms -Nchip-seq-data
dh_missing
dh_dwz
dh_strip
dh_makeshlibs
dh_shlibdeps
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
dh_installdeb
dh_gencontrol
dpkg-gencontrol: warning: package chip-seq: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package chip-seq: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums
dh_builddeb
dpkg-deb: building package 'chip-seq-data' in '../chip-seq-data_1.5.5-3_all.deb'.
dpkg-deb: building package 'chip-seq' in '../chip-seq_1.5.5-3_arm64.deb'.
dpkg-deb: building package 'chip-seq-dbgsym' in '../chip-seq-dbgsym_1.5.5-3_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../chip-seq_1.5.5-3_arm64.buildinfo
dpkg-genchanges --build=binary -O../chip-seq_1.5.5-3_arm64.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/2185971 and its subdirectories
I: Current time: Sat Feb 21 05:07:22 -12 2026
I: pbuilder-time-stamp: 1771693642
Sun Jan 19 10:44:25 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net.
Sun Jan 19 10:44:25 UTC 2025 I: Preparing to do remote build '2' on codethink01-arm64.debian.net.
Sun Jan 19 10:45:38 UTC 2025 I: Deleting $TMPDIR on codethink01-arm64.debian.net.
Sun Jan 19 10:45:39 UTC 2025 I: chip-seq_1.5.5-3_arm64.changes:
Format: 1.8
Date: Sun, 29 Mar 2020 12:44:42 +0200
Source: chip-seq
Binary: chip-seq chip-seq-data chip-seq-dbgsym
Architecture: all arm64
Version: 1.5.5-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
chip-seq - tools performing common ChIP-Seq data analysis tasks
chip-seq-data - tools performing common ChIP-Seq data analysis tasks (data)
Changes:
chip-seq (1.5.5-3) unstable; urgency=medium
.
* Fix arch only build
Checksums-Sha1:
747b5125f5190f61437a00fdf2be5ea1b4616363 3003644 chip-seq-data_1.5.5-3_all.deb
4fafe0f221c2b6d4c18d20bf15ee4536ddb72cf9 111204 chip-seq-dbgsym_1.5.5-3_arm64.deb
8dd9c88f782502195394fb28d9f5446899540c21 5250 chip-seq_1.5.5-3_arm64.buildinfo
96b180cdcf6097057290cb59a6486e80a45f9932 97648 chip-seq_1.5.5-3_arm64.deb
Checksums-Sha256:
f447726c1aeb4e7e74ab00ab9d244cb7e881555aae7a761538fab52d013383ff 3003644 chip-seq-data_1.5.5-3_all.deb
4f16f6ec9dadf6d3f6d1fd32777bf2f90c6a2b6624f97f095e3804f5a644374f 111204 chip-seq-dbgsym_1.5.5-3_arm64.deb
d8c8771b669bc44ac73c6b8a85e23db42925552f79862c6d69647384db9f14ec 5250 chip-seq_1.5.5-3_arm64.buildinfo
f58fc0a36b2aad204810f25da9306d5eca2eb278a014eb1e7f465daba8bb8752 97648 chip-seq_1.5.5-3_arm64.deb
Files:
ac9e1ca4ebdfa04beacaad8180d17898 3003644 science optional chip-seq-data_1.5.5-3_all.deb
3915b8eb8d961bd8509d5490f2a561ca 111204 debug optional chip-seq-dbgsym_1.5.5-3_arm64.deb
ad1ad4041cd741510784a83feae06319 5250 science optional chip-seq_1.5.5-3_arm64.buildinfo
034a7a452cf1e06db076aed0b6141747 97648 science optional chip-seq_1.5.5-3_arm64.deb
Sun Jan 19 10:45:40 UTC 2025 I: diffoscope 285 will be used to compare the two builds:
Running as unit: rb-diffoscope-arm64_5-78894.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ErUfD9wI/chip-seq_1.5.5-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ErUfD9wI/chip-seq_1.5.5-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ErUfD9wI/chip-seq_1.5.5-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ErUfD9wI/b1/chip-seq_1.5.5-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ErUfD9wI/b2/chip-seq_1.5.5-3_arm64.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: 0.399s)
0.399s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.042s)
0.042s 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: 707ms
CPU time consumed: 705ms
Sun Jan 19 10:45:42 UTC 2025 I: diffoscope 285 found no differences in the changes files, and a .buildinfo file also exists.
Sun Jan 19 10:45:42 UTC 2025 I: chip-seq from trixie built successfully and reproducibly on arm64.
Sun Jan 19 10:45:43 UTC 2025 I: Submitting .buildinfo files to external archives:
Sun Jan 19 10:45:43 UTC 2025 I: Submitting 8.0K b1/chip-seq_1.5.5-3_arm64.buildinfo.asc
Sun Jan 19 10:45:44 UTC 2025 I: Submitting 8.0K b2/chip-seq_1.5.5-3_arm64.buildinfo.asc
Sun Jan 19 10:45:46 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Jan 19 10:45:46 UTC 2025 I: Done submitting .buildinfo files.
Sun Jan 19 10:45:46 UTC 2025 I: Removing signed chip-seq_1.5.5-3_arm64.buildinfo.asc files:
removed './b1/chip-seq_1.5.5-3_arm64.buildinfo.asc'
removed './b2/chip-seq_1.5.5-3_arm64.buildinfo.asc'