Wed May 17 19:29:30 UTC 2023 I: starting to build bio-rainbow/bookworm/armhf on jenkins on '2023-05-17 19:29'
Wed May 17 19:29:30 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_43/6616/console.log
Wed May 17 19:29:30 UTC 2023 I: Downloading source for bookworm/bio-rainbow=2.0.4+dfsg-2
--2023-05-17 19:29:31-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/bio-rainbow/bio-rainbow_2.0.4%2bdfsg-2.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2094 (2.0K) [text/prs.lines.tag]
Saving to: ‘bio-rainbow_2.0.4+dfsg-2.dsc’
0K .. 100% 141M=0s
2023-05-17 19:29:31 (141 MB/s) - ‘bio-rainbow_2.0.4+dfsg-2.dsc’ saved [2094/2094]
Wed May 17 19:29:31 UTC 2023 I: bio-rainbow_2.0.4+dfsg-2.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: bio-rainbow
Binary: bio-rainbow
Architecture: any
Version: 2.0.4+dfsg-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Olivier Sallou <osallou@debian.org>, Pranav Ballaney <ballaneypranav@gmail.com>
Homepage: http://sourceforge.net/projects/bio-rainbow/
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/bio-rainbow
Vcs-Git: https://salsa.debian.org/med-team/bio-rainbow.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), help2man
Package-List:
bio-rainbow deb science optional arch=any
Checksums-Sha1:
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0167f4b007285a9c2f54f313a7a1c475aaebc0d5 14012 bio-rainbow_2.0.4+dfsg-2.debian.tar.xz
Checksums-Sha256:
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2ff6db13165339d6b52e13eea6ab32700a48c662d9409062a18cebe156836a36 14012 bio-rainbow_2.0.4+dfsg-2.debian.tar.xz
Files:
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cb7bb50a5910620b126226506cc13922 14012 bio-rainbow_2.0.4+dfsg-2.debian.tar.xz
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Wed May 17 19:29:31 UTC 2023 I: Checking whether the package is not for us
Wed May 17 19:29:31 UTC 2023 I: Starting 1st build on remote node jtx1b-armhf-rb.debian.net.
Wed May 17 19:29:31 UTC 2023 I: Preparing to do remote build '1' on jtx1b-armhf-rb.debian.net.
Wed May 17 19:30:51 UTC 2023 I: Deleting $TMPDIR on jtx1b-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Wed May 17 07:29:37 -12 2023
I: pbuilder-time-stamp: 1684351777
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-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 [bio-rainbow_2.0.4+dfsg-2.dsc]
I: copying [./bio-rainbow_2.0.4+dfsg.orig.tar.xz]
I: copying [./bio-rainbow_2.0.4+dfsg-2.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sun Aug 23 07:03:07 2020 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./bio-rainbow_2.0.4+dfsg-2.dsc: no acceptable signature found
dpkg-source: info: extracting bio-rainbow in bio-rainbow-2.0.4+dfsg
dpkg-source: info: unpacking bio-rainbow_2.0.4+dfsg.orig.tar.xz
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.creationtime'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
dpkg-source: info: unpacking bio-rainbow_2.0.4+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying add_hardening.patch
dpkg-source: info: applying rename_binary.patch
dpkg-source: info: applying spelling.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/6218/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
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='bookworm'
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='e17be88059a74094b0ae78cecb7c4919'
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='6218'
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.MuCKJ84F/pbuilderrc_CopJ --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MuCKJ84F/b1 --logfile b1/build.log bio-rainbow_2.0.4+dfsg-2.dsc'
SUDO_GID='114'
SUDO_UID='110'
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 jtx1b 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux
I: ls -l /bin
total 5072
-rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash
-rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 67632 Sep 20 2022 cat
-rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 67684 Sep 20 2022 chown
-rwxr-xr-x 1 root root 133532 Sep 20 2022 cp
-rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash
-rwxr-xr-x 1 root root 133220 Sep 20 2022 date
-rwxr-xr-x 1 root root 67732 Sep 20 2022 dd
-rwxr-xr-x 1 root root 68104 Sep 20 2022 df
-rwxr-xr-x 1 root root 133632 Sep 20 2022 dir
-rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname
-rwxr-xr-x 1 root root 67560 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep
-rwxr-xr-x 1 root root 67548 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep
-rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt
-rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount
-rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname
-rwxr-xr-x 1 root root 67720 Sep 20 2022 ln
-rwxr-xr-x 1 root root 35132 Mar 22 21:51 login
-rwxr-xr-x 1 root root 133632 Sep 20 2022 ls
-rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk
-rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 38504 Mar 22 21:02 more
-rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount
-rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint
-rwxr-xr-x 1 root root 133532 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash
-rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 67672 Sep 20 2022 rm
-rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed
lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash
-rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 67644 Sep 20 2022 stty
-rwsr-xr-x 1 root root 50800 Mar 22 21:02 su
-rwxr-xr-x 1 root root 67584 Sep 20 2022 sync
-rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar
-rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 133224 Sep 20 2022 touch
-rwxr-xr-x 1 root root 67548 Sep 20 2022 true
-rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server
-rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount
-rwxr-xr-x 1 root root 67572 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/6218/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), help2man
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19329 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 help2man; however:
Package help2man 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} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{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, 32 newly installed, 0 to remove and 0 not upgraded.
Need to get 18.3 MB of archives. After unpacking 68.4 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main armhf liblocale-gettext-perl armhf 1.07-5 [14.9 kB]
Get: 2 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 3 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB]
Get: 4 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB]
Get: 5 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB]
Get: 6 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB]
Get: 7 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get: 8 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB]
Get: 9 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB]
Get: 10 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB]
Get: 11 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB]
Get: 12 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB]
Get: 13 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB]
Get: 14 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 15 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 16 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB]
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Get: 26 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB]
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Get: 28 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB]
Get: 29 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB]
Get: 32 http://deb.debian.org/debian bookworm/main armhf help2man armhf 1.49.3 [198 kB]
Fetched 18.3 MB in 2s (11.1 MB/s)
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I: Building the package
I: Running cd /build/bio-rainbow-2.0.4+dfsg/ && 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 > ../bio-rainbow_2.0.4+dfsg-2_source.changes
dpkg-buildpackage: info: source package bio-rainbow
dpkg-buildpackage: info: source version 2.0.4+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Pranav Ballaney <ballaneypranav@gmail.com>
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/bio-rainbow-2.0.4+dfsg'
rm -f *.o *.gcda *.gcno *.gcov gmon.out bio-rainbow rbasm ezmsim rbmergetag *.exe
make[1]: Leaving directory '/build/bio-rainbow-2.0.4+dfsg'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j3 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/bio-rainbow-2.0.4+dfsg'
gcc -c -g -O2 -ffile-prefix-map=/build/bio-rainbow-2.0.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 main.c -o main.o
gcc -c -g -O2 -ffile-prefix-map=/build/bio-rainbow-2.0.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 divide.c -o divide.o
gcc -c -g -O2 -ffile-prefix-map=/build/bio-rainbow-2.0.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 file_reader.c -o file_reader.o
file_reader.c: In function 'fopen_m_filereader':
file_reader.c:38:48: warning: '%s' directive writing between 4 and 2147483645 bytes into a region of size 2147483638 [-Wformat-overflow=]
38 | sprintf(cmd, "gzip -dc %s", filenames[i]);
| ^~
In file included from /usr/include/stdio.h:906,
from file_reader.h:22,
from file_reader.c:20:
In function 'sprintf',
inlined from 'fopen_m_filereader' at file_reader.c:38:4:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 14 and 2147483655 bytes into a destination of size 2147483647
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -c -g -O2 -ffile-prefix-map=/build/bio-rainbow-2.0.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 asm_R2.c -o asm_R2.o
At top level:
cc1: note: unrecognized command-line option '-Wno-self-assign' may have been intended to silence earlier diagnostics
gcc -c -g -O2 -ffile-prefix-map=/build/bio-rainbow-2.0.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 mergectg.c -o mergectg.o
gcc -c -g -O2 -ffile-prefix-map=/build/bio-rainbow-2.0.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 cluster.c -o cluster.o
gcc -c -g -O2 -ffile-prefix-map=/build/bio-rainbow-2.0.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 ezmsim.c -o ezmsim.o
ezmsim.c: In function 'LR_main':
ezmsim.c:440:33: warning: this statement may fall through [-Wimplicit-fallthrough=]
440 | case 'z': cut = strdup(optarg);
| ^~~~~~~~~~~~~~
ezmsim.c:441:17: note: here
441 | case 'p': pos = atoi(optarg);
| ^~~~
ezmsim.c: In function 'EF_main':
ezmsim.c:707:33: warning: this statement may fall through [-Wimplicit-fallthrough=]
707 | case 'z': cut = strdup(optarg);
| ^~~~~~~~~~~~~~
ezmsim.c:708:17: note: here
708 | case 'p': pos = atoi(optarg);
| ^~~~
gcc -c -g -O2 -ffile-prefix-map=/build/bio-rainbow-2.0.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -D_FILE_OFFSET_BITS=64 rbasm_main.c -o rbasm_main.o
gcc -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bio-rainbow-2.0.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -o rbasm asm_R2.o rbasm_main.o file_reader.o -lm
gcc -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bio-rainbow-2.0.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -o bio-rainbow main.o divide.o file_reader.o asm_R2.o mergectg.o cluster.o -lm
At top level:
cc1: note: unrecognized command-line option '-Wno-self-assign' may have been intended to silence earlier diagnostics
gcc -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/bio-rainbow-2.0.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -O2 -Wall -Wno-self-assign -Wno-unused-function -o ezmsim ezmsim.o -lm
make[1]: Leaving directory '/build/bio-rainbow-2.0.4+dfsg'
dh_auto_test
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/bio-rainbow/
dh_install
dh_installdocs
dh_installchangelogs
dh_installexamples
debian/rules override_dh_installman
make[1]: Entering directory '/build/bio-rainbow-2.0.4+dfsg'
# dh_installman is messing up .sh extension as language extension
dh_install debian/mans/*.1 usr/share/man/man1
make[1]: Leaving directory '/build/bio-rainbow-2.0.4+dfsg'
dh_lintian
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 'bio-rainbow-dbgsym' in '../bio-rainbow-dbgsym_2.0.4+dfsg-2_armhf.deb'.
dpkg-deb: building package 'bio-rainbow' in '../bio-rainbow_2.0.4+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=binary -O../bio-rainbow_2.0.4+dfsg-2_armhf.buildinfo
dpkg-genchanges --build=binary -O../bio-rainbow_2.0.4+dfsg-2_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: 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/6218 and its subdirectories
I: Current time: Wed May 17 07:30:47 -12 2023
I: pbuilder-time-stamp: 1684351847
Wed May 17 19:30:54 UTC 2023 I: 1st build successful. Starting 2nd build on remote node cbxi4pro0-armhf-rb.debian.net.
Wed May 17 19:30:54 UTC 2023 I: Preparing to do remote build '2' on cbxi4pro0-armhf-rb.debian.net.
Wed May 17 19:36:25 UTC 2023 I: Deleting $TMPDIR on cbxi4pro0-armhf-rb.debian.net.
Wed May 17 19:36:28 UTC 2023 I: bio-rainbow_2.0.4+dfsg-2_armhf.changes:
Format: 1.8
Date: Sun, 23 Aug 2020 05:32:47 +0530
Source: bio-rainbow
Binary: bio-rainbow bio-rainbow-dbgsym
Architecture: armhf
Version: 2.0.4+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Pranav Ballaney <ballaneypranav@gmail.com>
Description:
bio-rainbow - clustering and assembling short reads for bioinformatics
Changes:
bio-rainbow (2.0.4+dfsg-2) unstable; urgency=medium
.
[ Steffen Möller ]
* Updated bio.tools ref
* Added ref to conda
.
[ Pranav Ballaney ]
* Install data for autopkgtests
* Add autopkgtests
* Install docs
* Add Pranav Ballaney to Uploaders
* Standards-Version: 4.5.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Remove trailing whitespace in debian/rules (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
Checksums-Sha1:
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f31767bb4a860053195455c37c00b9d04a4b5897 5096 bio-rainbow_2.0.4+dfsg-2_armhf.buildinfo
f70111bc3542503d1425872c23a1a1ed40e59613 55592 bio-rainbow_2.0.4+dfsg-2_armhf.deb
Checksums-Sha256:
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e37a4413ca41b8e0b09164ca07fa339566305ab4e5b0f039bc36ff5ced3d1278 5096 bio-rainbow_2.0.4+dfsg-2_armhf.buildinfo
c9daec979565cc0174f10269a7238ca5b1961083469c3ba31a44039ad5caaf17 55592 bio-rainbow_2.0.4+dfsg-2_armhf.deb
Files:
d2801683f6a0c56e47489edeb9df3970 169632 debug optional bio-rainbow-dbgsym_2.0.4+dfsg-2_armhf.deb
17b250fdeeecf1bb81c05dda7c0e29e7 5096 science optional bio-rainbow_2.0.4+dfsg-2_armhf.buildinfo
dd8cb7a2b7a70ce361232c9033658e1b 55592 science optional bio-rainbow_2.0.4+dfsg-2_armhf.deb
Wed May 17 19:36:29 UTC 2023 I: diffoscope 242 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.MuCKJ84F/bio-rainbow_2.0.4+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.MuCKJ84F/bio-rainbow_2.0.4+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.MuCKJ84F/bio-rainbow_2.0.4+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.MuCKJ84F/b1/bio-rainbow_2.0.4+dfsg-2_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.MuCKJ84F/b2/bio-rainbow_2.0.4+dfsg-2_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: 0.316s)
0.316s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.018s)
0.018s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Wed May 17 19:36:30 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists.
Wed May 17 19:36:30 UTC 2023 I: bio-rainbow from bookworm built successfully and reproducibly on armhf.
Wed May 17 19:36:31 UTC 2023 I: Submitting .buildinfo files to external archives:
Wed May 17 19:36:31 UTC 2023 I: Submitting 8.0K b1/bio-rainbow_2.0.4+dfsg-2_armhf.buildinfo.asc
Wed May 17 19:36:32 UTC 2023 I: Submitting 8.0K b2/bio-rainbow_2.0.4+dfsg-2_armhf.buildinfo.asc
Wed May 17 19:36:34 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Wed May 17 19:36:34 UTC 2023 I: Done submitting .buildinfo files.
Wed May 17 19:36:34 UTC 2023 I: Removing signed bio-rainbow_2.0.4+dfsg-2_armhf.buildinfo.asc files:
removed './b1/bio-rainbow_2.0.4+dfsg-2_armhf.buildinfo.asc'
removed './b2/bio-rainbow_2.0.4+dfsg-2_armhf.buildinfo.asc'