Sun Jan 7 16:25:47 UTC 2024 I: starting to build peptidebuilder/bookworm/i386 on jenkins on '2024-01-07 16:25'
Sun Jan 7 16:25:47 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_7/13816/console.log
Sun Jan 7 16:25:47 UTC 2024 I: Downloading source for bookworm/peptidebuilder=1.1.0-3
--2024-01-07 16:25:47-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/peptidebuilder/peptidebuilder_1.1.0-3.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2239 (2.2K) [text/prs.lines.tag]
Saving to: ‘peptidebuilder_1.1.0-3.dsc’
0K .. 100% 171M=0s
2024-01-07 16:25:47 (171 MB/s) - ‘peptidebuilder_1.1.0-3.dsc’ saved [2239/2239]
Sun Jan 7 16:25:47 UTC 2024 I: peptidebuilder_1.1.0-3.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: peptidebuilder
Binary: python3-peptidebuilder
Architecture: all
Version: 1.1.0-3
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>, Nilesh Patra <nilesh@debian.org>
Homepage: https://github.com/clauswilke/PeptideBuilder/
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/peptidebuilder
Vcs-Git: https://salsa.debian.org/med-team/peptidebuilder.git
Testsuite: autopkgtest
Testsuite-Triggers: python3
Build-Depends: debhelper-compat (= 13), dh-python, python3-setuptools, python3-all, python3-biopython, python3-pytest <!nocheck>, python3-pytest-cov <!nocheck>
Package-List:
python3-peptidebuilder deb science optional arch=all
Checksums-Sha1:
a85fb4c9ed7ec362ae5ec59de54494bea15572a9 467902 peptidebuilder_1.1.0.orig.tar.gz
54117dfe573dcffca22d791cae9fbf5b563258b8 4016 peptidebuilder_1.1.0-3.debian.tar.xz
Checksums-Sha256:
382b43fd118a3a7668fb03ecc07d8ffff6b8b522e687e4902d9f854426011e6d 467902 peptidebuilder_1.1.0.orig.tar.gz
8569e090c1ca19012108e18a45636d3189e57a6b124fdd8e70044ea362dde5a3 4016 peptidebuilder_1.1.0-3.debian.tar.xz
Files:
eee55fc2ed9e7a588483942dce64ae56 467902 peptidebuilder_1.1.0.orig.tar.gz
e4fd36c0b9a8d0100c8fb8ff60195bf4 4016 peptidebuilder_1.1.0-3.debian.tar.xz
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Sun Jan 7 16:25:47 UTC 2024 I: Checking whether the package is not for us
Sun Jan 7 16:25:47 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net.
Sun Jan 7 16:25:47 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net.
Sun Jan 7 16:27:59 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun Jan 7 04:25:50 -12 2024
I: pbuilder-time-stamp: 1704644750
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: using eatmydata during job
I: Copying source file
I: copying [peptidebuilder_1.1.0-3.dsc]
I: copying [./peptidebuilder_1.1.0.orig.tar.gz]
I: copying [./peptidebuilder_1.1.0-3.debian.tar.xz]
I: Extracting source
gpgv: Signature made Fri Oct 8 20:54:03 2021
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 ./peptidebuilder_1.1.0-3.dsc: no acceptable signature found
dpkg-source: info: extracting peptidebuilder in peptidebuilder-1.1.0
dpkg-source: info: unpacking peptidebuilder_1.1.0.orig.tar.gz
dpkg-source: info: unpacking peptidebuilder_1.1.0-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix-paths-with-os.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/12488/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='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 '
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='10508e9ca13748658c01f57d1c025843'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
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='12488'
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.XB5lODhk/pbuilderrc_9ddR --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.XB5lODhk/b1 --logfile b1/build.log peptidebuilder_1.1.0-3.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://78.137.99.97:3128'
I: uname -a
Linux ionos12-i386 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux
I: ls -l /bin
total 6036
-rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2
-rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore
-rwxr-xr-x 1 root root 42920 Sep 20 2022 cat
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chown
-rwxr-xr-x 1 root root 162024 Sep 20 2022 cp
-rwxr-xr-x 1 root root 136916 Jan 5 2023 dash
-rwxr-xr-x 1 root root 137160 Sep 20 2022 date
-rwxr-xr-x 1 root root 100364 Sep 20 2022 dd
-rwxr-xr-x 1 root root 108940 Sep 20 2022 df
-rwxr-xr-x 1 root root 162152 Sep 20 2022 dir
-rwxr-xr-x 1 root root 87760 Mar 23 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname
-rwxr-xr-x 1 root root 38760 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 2023 egrep
-rwxr-xr-x 1 root root 34664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep
-rwxr-xr-x 1 root root 84272 Mar 23 2023 findmnt
-rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount
-rwxr-xr-x 1 root root 218680 Jan 24 2023 grep
-rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe
-rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip
-rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname
-rwxr-xr-x 1 root root 75756 Sep 20 2022 ln
-rwxr-xr-x 1 root root 55600 Mar 23 2023 login
-rwxr-xr-x 1 root root 162152 Sep 20 2022 ls
-rwxr-xr-x 1 root root 214568 Mar 23 2023 lsblk
-rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 63016 Mar 23 2023 more
-rwsr-xr-x 1 root root 58912 Mar 23 2023 mount
-rwxr-xr-x 1 root root 13856 Mar 23 2023 mountpoint
-rwxr-xr-x 1 root root 157932 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash
-rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 20 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 22308 Jul 28 23:46 run-parts
-rwxr-xr-x 1 root root 133224 Jan 5 2023 sed
lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash
-rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 20 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 23 2023 su
-rwxr-xr-x 1 root root 38792 Sep 20 2022 sync
-rwxr-xr-x 1 root root 598456 Apr 6 2023 tar
-rwxr-xr-x 1 root root 13860 Jul 28 23:46 tempfile
-rwxr-xr-x 1 root root 120776 Sep 20 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 20 2022 true
-rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Mar 23 2023 umount
-rwxr-xr-x 1 root root 38760 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress
-rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 71216 Mar 23 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 10 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 10 2022 znew
I: user script /srv/workspace/pbuilder/12488/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: i386
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), dh-python, python3-setuptools, python3-all, python3-biopython, python3-pytest, python3-pytest-cov
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 18156 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 dh-python; however:
Package dh-python is not installed.
pbuilder-satisfydepends-dummy depends on python3-setuptools; however:
Package python3-setuptools is not installed.
pbuilder-satisfydepends-dummy depends on python3-all; however:
Package python3-all is not installed.
pbuilder-satisfydepends-dummy depends on python3-biopython; however:
Package python3-biopython is not installed.
pbuilder-satisfydepends-dummy depends on python3-pytest; however:
Package python3-pytest is not installed.
pbuilder-satisfydepends-dummy depends on python3-pytest-cov; however:
Package python3-pytest-cov 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-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-hotkeys{a} libjs-jquery-isonscreen{a} libjs-jquery-metadata{a} libjs-jquery-tablesorter{a} libjs-jquery-throttle-debounce{a} liblapack3{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1{a} libopenjp2-7{a} libpipeline1{a} libpng16-16{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libraqm0{a} libreadline8{a} libsub-override-perl{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} po-debconf{a} python3{a} python3-all{a} python3-attr{a} python3-biopython{a} python3-coverage{a} python3-distutils{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-py{a} python3-pytest{a} python3-pytest-cov{a} python3-renderpm{a} python3-reportlab{a} python3-reportlab-accel{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl javascript-common libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-olefile python3-pygments shared-mime-info wget xdg-user-dirs
0 packages upgraded, 104 newly installed, 0 to remove and 0 not upgraded.
Need to get 57.5 MB of archives. After unpacking 203 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 2 http://deb.debian.org/debian bookworm/main i386 libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB]
Get: 3 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 mailcap all 3.70+nmu1 [32.0 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 mime-support all 3.66 [10.9 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB]
Get: 11 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB]
Get: 13 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B]
Get: 15 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 sgml-base all 1.31 [15.4 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 21 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 22 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 23 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 24 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 26 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 31 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 32 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 33 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 34 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 35 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 36 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 37 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 38 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 39 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 40 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 41 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 42 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.3~deb12u1 [720 kB]
Get: 43 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 44 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 45 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 46 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Get: 47 http://deb.debian.org/debian bookworm/main i386 python3-lib2to3 all 3.11.2-3 [76.3 kB]
Get: 48 http://deb.debian.org/debian bookworm/main i386 python3-distutils all 3.11.2-3 [131 kB]
Get: 49 http://deb.debian.org/debian bookworm/main i386 dh-python all 5.20230130+deb12u1 [104 kB]
Get: 50 http://deb.debian.org/debian bookworm/main i386 libfontenc1 i386 1:1.1.4-1 [24.5 kB]
Get: 51 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB]
Get: 52 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB]
Get: 53 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-5 [410 kB]
Get: 54 http://deb.debian.org/debian bookworm/main i386 x11-common all 1:7.7+23 [252 kB]
Get: 55 http://deb.debian.org/debian bookworm/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get: 56 http://deb.debian.org/debian bookworm/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB]
Get: 57 http://deb.debian.org/debian bookworm/main i386 fonts-urw-base35 all 20200910-7 [10.8 MB]
Get: 58 http://deb.debian.org/debian bookworm/main i386 libblas3 i386 3.11.0-2 [139 kB]
Get: 59 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB]
Get: 60 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB]
Get: 61 http://deb.debian.org/debian bookworm/main i386 libfribidi0 i386 1.0.8-2.1 [65.6 kB]
Get: 62 http://deb.debian.org/debian bookworm/main i386 libgfortran5 i386 12.2.0-14 [698 kB]
Get: 63 http://deb.debian.org/debian bookworm/main i386 libglib2.0-0 i386 2.74.6-2 [1467 kB]
Get: 64 http://deb.debian.org/debian bookworm/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB]
Get: 65 http://deb.debian.org/debian bookworm/main i386 libharfbuzz0b i386 6.0.0+dfsg-3 [1966 kB]
Get: 66 http://deb.debian.org/debian bookworm/main i386 libimagequant0 i386 2.17.0-1 [32.9 kB]
Get: 67 http://deb.debian.org/debian bookworm/main i386 libjbig0 i386 2.1-6.1 [31.6 kB]
Get: 68 http://deb.debian.org/debian bookworm/main i386 libjpeg62-turbo i386 1:2.1.5-2 [169 kB]
Get: 69 http://deb.debian.org/debian bookworm/main i386 libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B]
Get: 70 http://deb.debian.org/debian bookworm/main i386 libjs-jquery-metadata all 12-4 [6532 B]
Get: 71 http://deb.debian.org/debian bookworm/main i386 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-3 [184 kB]
Get: 72 http://deb.debian.org/debian bookworm/main i386 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB]
Get: 73 http://deb.debian.org/debian bookworm/main i386 liblapack3 i386 3.11.0-2 [2092 kB]
Get: 74 http://deb.debian.org/debian bookworm/main i386 liblcms2-2 i386 2.14-2 [165 kB]
Get: 75 http://deb.debian.org/debian bookworm/main i386 liblerc4 i386 4.0.0+ds-2 [181 kB]
Get: 76 http://deb.debian.org/debian bookworm/main i386 libopenjp2-7 i386 2.5.0-2 [196 kB]
Get: 77 http://deb.debian.org/debian bookworm/main i386 libraqm0 i386 0.7.0-4.1 [11.1 kB]
Get: 78 http://deb.debian.org/debian bookworm/main i386 libwebp7 i386 1.2.4-0.2+deb12u1 [294 kB]
Get: 79 http://deb.debian.org/debian bookworm/main i386 libtiff6 i386 4.5.0-6+deb12u1 [332 kB]
Get: 80 http://deb.debian.org/debian bookworm/main i386 libwebpdemux2 i386 1.2.4-0.2+deb12u1 [99.8 kB]
Get: 81 http://deb.debian.org/debian bookworm/main i386 libwebpmux3 i386 1.2.4-0.2+deb12u1 [111 kB]
Get: 82 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB]
Get: 83 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB]
Get: 84 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB]
Get: 85 http://deb.debian.org/debian bookworm/main i386 python3-all i386 3.11.2-1+b1 [1056 B]
Get: 86 http://deb.debian.org/debian bookworm/main i386 python3-attr all 22.2.0-1 [65.4 kB]
Get: 87 http://deb.debian.org/debian bookworm/main i386 python3-pkg-resources all 66.1.1-1 [296 kB]
Get: 88 http://deb.debian.org/debian bookworm/main i386 python3-numpy i386 1:1.24.2-1 [6115 kB]
Get: 89 http://deb.debian.org/debian bookworm/main i386 python3-renderpm i386 3.6.12-1+b1 [81.4 kB]
Get: 90 http://deb.debian.org/debian bookworm/main i386 python3-reportlab-accel i386 3.6.12-1+b1 [39.4 kB]
Get: 91 http://deb.debian.org/debian bookworm/main i386 python3-pil i386 9.4.0-1.1+b1 [473 kB]
Get: 92 http://deb.debian.org/debian bookworm/main i386 python3-reportlab all 3.6.12-1 [564 kB]
Get: 93 http://deb.debian.org/debian bookworm/main i386 xml-core all 0.18+nmu1 [23.8 kB]
Get: 94 http://deb.debian.org/debian bookworm/main i386 w3c-sgml-lib all 1.3-3 [273 kB]
Get: 95 http://deb.debian.org/debian bookworm/main i386 python3-biopython i386 1.80+dfsg-4+b1 [1589 kB]
Get: 96 http://deb.debian.org/debian bookworm/main i386 python3-coverage i386 6.5.0+dfsg1-2+b1 [153 kB]
Get: 97 http://deb.debian.org/debian bookworm/main i386 python3-iniconfig all 1.1.1-2 [6396 B]
Get: 98 http://deb.debian.org/debian bookworm/main i386 python3-more-itertools all 8.10.0-2 [53.0 kB]
Get: 99 http://deb.debian.org/debian bookworm/main i386 python3-packaging all 23.0-1 [32.5 kB]
Get: 100 http://deb.debian.org/debian bookworm/main i386 python3-pluggy all 1.0.0+repack-1 [19.7 kB]
Get: 101 http://deb.debian.org/debian bookworm/main i386 python3-py all 1.11.0-1 [89.2 kB]
Get: 102 http://deb.debian.org/debian bookworm/main i386 python3-pytest all 7.2.1-2 [236 kB]
Get: 103 http://deb.debian.org/debian bookworm/main i386 python3-pytest-cov all 4.0.0-1 [26.1 kB]
Get: 104 http://deb.debian.org/debian bookworm/main i386 python3-setuptools all 66.1.1-1 [521 kB]
Fetched 57.5 MB in 5s (10.9 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libjs-jquery.
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Unpacking libreadline8:i386 (8.2-1.3) ...
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Unpacking python3.11 (3.11.2-6) ...
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Unpacking python3 (3.11.2-1+b1) ...
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Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:i386.
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Unpacking libmagic1:i386 (1:5.44-3) ...
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Selecting previously unselected package libuchardet0:i386.
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Unpacking m4 (1.4.19-3) ...
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Selecting previously unselected package libfontenc1:i386.
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Unpacking libpng16-16:i386 (1.6.39-2) ...
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Unpacking libfreetype6:i386 (2.12.1+dfsg-5) ...
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Unpacking x11-common (1:7.7+23) ...
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Unpacking xfonts-encodings (1:1.0.4-2.2) ...
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Unpacking xfonts-utils (1:7.7+6) ...
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Unpacking libglib2.0-0:i386 (2.74.6-2) ...
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Selecting previously unselected package libharfbuzz0b:i386.
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Selecting previously unselected package libimagequant0:i386.
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Unpacking libjbig0:i386 (2.1-6.1) ...
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Unpacking libjs-jquery-metadata (12-4) ...
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Unpacking libjs-jquery-tablesorter (1:2.31.3+dfsg1-3) ...
Selecting previously unselected package libjs-jquery-throttle-debounce.
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Unpacking libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ...
Selecting previously unselected package liblapack3:i386.
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Unpacking liblapack3:i386 (3.11.0-2) ...
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Unpacking liblcms2-2:i386 (2.14-2) ...
Selecting previously unselected package liblerc4:i386.
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Unpacking liblerc4:i386 (4.0.0+ds-2) ...
Selecting previously unselected package libopenjp2-7:i386.
Preparing to unpack .../61-libopenjp2-7_2.5.0-2_i386.deb ...
Unpacking libopenjp2-7:i386 (2.5.0-2) ...
Selecting previously unselected package libraqm0:i386.
Preparing to unpack .../62-libraqm0_0.7.0-4.1_i386.deb ...
Unpacking libraqm0:i386 (0.7.0-4.1) ...
Selecting previously unselected package libwebp7:i386.
Preparing to unpack .../63-libwebp7_1.2.4-0.2+deb12u1_i386.deb ...
Unpacking libwebp7:i386 (1.2.4-0.2+deb12u1) ...
Selecting previously unselected package libtiff6:i386.
Preparing to unpack .../64-libtiff6_4.5.0-6+deb12u1_i386.deb ...
Unpacking libtiff6:i386 (4.5.0-6+deb12u1) ...
Selecting previously unselected package libwebpdemux2:i386.
Preparing to unpack .../65-libwebpdemux2_1.2.4-0.2+deb12u1_i386.deb ...
Unpacking libwebpdemux2:i386 (1.2.4-0.2+deb12u1) ...
Selecting previously unselected package libwebpmux3:i386.
Preparing to unpack .../66-libwebpmux3_1.2.4-0.2+deb12u1_i386.deb ...
Unpacking libwebpmux3:i386 (1.2.4-0.2+deb12u1) ...
Selecting previously unselected package libxau6:i386.
Preparing to unpack .../67-libxau6_1%3a1.0.9-1_i386.deb ...
Unpacking libxau6:i386 (1:1.0.9-1) ...
Selecting previously unselected package libxdmcp6:i386.
Preparing to unpack .../68-libxdmcp6_1%3a1.1.2-3_i386.deb ...
Unpacking libxdmcp6:i386 (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:i386.
Preparing to unpack .../69-libxcb1_1.15-1_i386.deb ...
Unpacking libxcb1:i386 (1.15-1) ...
Selecting previously unselected package python3-all.
Preparing to unpack .../70-python3-all_3.11.2-1+b1_i386.deb ...
Unpacking python3-all (3.11.2-1+b1) ...
Selecting previously unselected package python3-attr.
Preparing to unpack .../71-python3-attr_22.2.0-1_all.deb ...
Unpacking python3-attr (22.2.0-1) ...
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Unpacking python3-pkg-resources (66.1.1-1) ...
Selecting previously unselected package python3-numpy.
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Unpacking python3-numpy (1:1.24.2-1) ...
Selecting previously unselected package python3-renderpm:i386.
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Unpacking python3-renderpm:i386 (3.6.12-1+b1) ...
Selecting previously unselected package python3-reportlab-accel:i386.
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Unpacking python3-reportlab-accel:i386 (3.6.12-1+b1) ...
Selecting previously unselected package python3-pil:i386.
Preparing to unpack .../76-python3-pil_9.4.0-1.1+b1_i386.deb ...
Unpacking python3-pil:i386 (9.4.0-1.1+b1) ...
Selecting previously unselected package python3-reportlab.
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Unpacking python3-reportlab (3.6.12-1) ...
Selecting previously unselected package xml-core.
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Unpacking xml-core (0.18+nmu1) ...
Selecting previously unselected package w3c-sgml-lib.
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Unpacking w3c-sgml-lib (1.3-3) ...
Selecting previously unselected package python3-biopython.
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Unpacking python3-biopython (1.80+dfsg-4+b1) ...
Selecting previously unselected package python3-coverage.
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Unpacking python3-coverage (6.5.0+dfsg1-2+b1) ...
Selecting previously unselected package python3-iniconfig.
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Unpacking python3-iniconfig (1.1.1-2) ...
Selecting previously unselected package python3-more-itertools.
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Unpacking python3-more-itertools (8.10.0-2) ...
Selecting previously unselected package python3-packaging.
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Unpacking python3-packaging (23.0-1) ...
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Unpacking python3-pluggy (1.0.0+repack-1) ...
Selecting previously unselected package python3-py.
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Unpacking python3-py (1.11.0-1) ...
Selecting previously unselected package python3-pytest.
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Unpacking python3-pytest (7.2.1-2) ...
Selecting previously unselected package python3-pytest-cov.
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Selecting previously unselected package python3-setuptools.
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Unpacking python3-setuptools (66.1.1-1) ...
Setting up media-types (10.0.0) ...
Setting up libpipeline1:i386 (1.5.7-1) ...
Setting up libgraphite2-3:i386 (1.3.14-1) ...
Setting up liblcms2-2:i386 (2.14-2) ...
Setting up libxau6:i386 (1:1.0.9-1) ...
Setting up libicu72:i386 (72.1-3) ...
Setting up liblerc4:i386 (4.0.0+ds-2) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:i386 (2.74.6-2) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.11.4) ...
Setting up libbrotli1:i386 (1.0.9-2+b6) ...
Setting up x11-common (1:7.7+23) ...
invoke-rc.d: could not determine current runlevel
Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix.
Setting up libmagic1:i386 (1:5.44-3) ...
Setting up libdeflate0:i386 (1.14-1) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up file (1:5.44-3) ...
Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ...
Setting up libjbig0:i386 (2.1-6.1) ...
Setting up libfontenc1:i386 (1:1.1.4-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libblas3:i386 (3.11.0-2) ...
update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode
Setting up libjpeg62-turbo:i386 (1:2.1.5-2) ...
Setting up xfonts-encodings (1:1.0.4-2.2) ...
Setting up libfribidi0:i386 (1.0.8-2.1) ...
Setting up libimagequant0:i386 (2.17.0-1) ...
Setting up libpng16-16:i386 (1.6.39-2) ...
Setting up autopoint (0.21-12) ...
Setting up libgfortran5:i386 (12.2.0-14) ...
Setting up autoconf (2.71-3) ...
Setting up libwebp7:i386 (1.2.4-0.2+deb12u1) ...
Setting up sensible-utils (0.0.17+nmu1) ...
Setting up libtiff6:i386 (4.5.0-6+deb12u1) ...
Setting up libuchardet0:i386 (0.0.7-1) ...
Setting up libopenjp2-7:i386 (2.5.0-2) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up sgml-base (1.31) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ...
Setting up libwebpmux3:i386 (1.2.4-0.2+deb12u1) ...
Setting up libbsd0:i386 (0.11.7-2) ...
Setting up mailcap (3.70+nmu1) ...
Setting up libelf1:i386 (0.188-2.1) ...
Setting up readline-common (8.2-1.3) ...
Setting up libxml2:i386 (2.9.14+dfsg-1.3~deb12u1) ...
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 (1.13.1-1) ...
Setting up libxdmcp6:i386 (1:1.1.2-3) ...
Setting up liblapack3:i386 (3.11.0-2) ...
update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode
Setting up libxcb1:i386 (1.15-1) ...
Setting up gettext (0.21-12) ...
Setting up mime-support (3.66) ...
Setting up libtool (2.4.7-5) ...
Setting up libwebpdemux2:i386 (1.2.4-0.2+deb12u1) ...
Setting up libreadline8:i386 (8.2-1.3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libfreetype6:i386 (2.12.1+dfsg-5) ...
Setting up libjs-jquery-metadata (12-4) ...
Setting up libjs-jquery-isonscreen (1.2.0-1.1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-3) ...
Setting up groff-base (1.22.4-10) ...
Setting up xml-core (0.18+nmu1) ...
Setting up libharfbuzz0b:i386 (6.0.0+dfsg-3) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libpython3.11-stdlib:i386 (3.11.2-6) ...
Setting up xfonts-utils (1:7.7+6) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libraqm0:i386 (0.7.0-4.1) ...
Setting up libpython3-stdlib:i386 (3.11.2-1+b1) ...
Setting up python3.11 (3.11.2-6) ...
Setting up debhelper (13.11.4) ...
Setting up python3 (3.11.2-1+b1) ...
Setting up fonts-urw-base35 (20200910-7) ...
Setting up python3-pil:i386 (9.4.0-1.1+b1) ...
Setting up python3-packaging (23.0-1) ...
Setting up python3-reportlab-accel:i386 (3.6.12-1+b1) ...
Setting up python3-pluggy (1.0.0+repack-1) ...
Setting up python3-reportlab (3.6.12-1) ...
Setting up python3-lib2to3 (3.11.2-3) ...
Setting up python3-pkg-resources (66.1.1-1) ...
Setting up python3-distutils (3.11.2-3) ...
Setting up dh-python (5.20230130+deb12u1) ...
Setting up python3-more-itertools (8.10.0-2) ...
Setting up python3-iniconfig (1.1.1-2) ...
Setting up python3-attr (22.2.0-1) ...
Setting up python3-renderpm:i386 (3.6.12-1+b1) ...
Setting up python3-setuptools (66.1.1-1) ...
Setting up python3-py (1.11.0-1) ...
Setting up python3-pytest (7.2.1-2) ...
Setting up python3-all (3.11.2-1+b1) ...
Setting up python3-coverage (6.5.0+dfsg1-2+b1) ...
Setting up python3-pytest-cov (4.0.0-1) ...
Setting up python3-numpy (1:1.24.2-1) ...
Processing triggers for libc-bin (2.36-9+deb12u3) ...
Processing triggers for sgml-base (1.31) ...
Setting up w3c-sgml-lib (1.3-3) ...
Setting up python3-biopython (1.80+dfsg-4+b1) ...
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/peptidebuilder-1.1.0/ && 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 > ../peptidebuilder_1.1.0-3_source.changes
dpkg-buildpackage: info: source package peptidebuilder
dpkg-buildpackage: info: source version 1.1.0-3
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 i386
dpkg-source: info: using options from peptidebuilder-1.1.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
debian/rules clean
dh clean --with python3 --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
pybuild --clean -i python{version} -p 3.11
I: pybuild base:240: python3.11 setup.py clean
running clean
removing '/build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.11_peptidebuilder/build' (and everything under it)
'build/bdist.linux-i386' does not exist -- can't clean it
'build/scripts-3.11' does not exist -- can't clean it
rm -rf .pybuild/
find . -name \*.pyc -exec rm {} \;
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/python3-peptidebuilder.substvars debian/files
rm -fr -- debian/python3-peptidebuilder/ debian/tmp/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary --with python3 --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
pybuild --configure -i python{version} -p 3.11
I: pybuild base:240: python3.11 setup.py config
running config
dh_auto_build -O--buildsystem=pybuild
pybuild --build -i python{version} -p 3.11
I: pybuild base:240: /usr/bin/python3 setup.py build
running build
running build_py
creating /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.11_peptidebuilder/build/PeptideBuilder
copying PeptideBuilder/__init__.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.11_peptidebuilder/build/PeptideBuilder
copying PeptideBuilder/PeptideBuilder.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.11_peptidebuilder/build/PeptideBuilder
copying PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.11_peptidebuilder/build/PeptideBuilder
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/peptidebuilder-1.1.0'
PYTHONPATH=$(pwd) pytest-3
============================= test session starts ==============================
platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack -- /usr/bin/python3
cachedir: .pytest_cache
rootdir: /build/reproducible-path/peptidebuilder-1.1.0, configfile: pytest.ini, testpaths: tests
plugins: cov-4.0.0
collecting ... collected 28 items
tests/test_Geometry.py::test_geometry_A PASSED [ 3%]
tests/test_Geometry.py::test_geometry_C PASSED [ 7%]
tests/test_Geometry.py::test_geometry_D PASSED [ 10%]
tests/test_Geometry.py::test_geometry_E PASSED [ 14%]
tests/test_Geometry.py::test_geometry_F PASSED [ 17%]
tests/test_Geometry.py::test_geometry_G PASSED [ 21%]
tests/test_Geometry.py::test_geometry_H PASSED [ 25%]
tests/test_Geometry.py::test_geometry_I PASSED [ 28%]
tests/test_Geometry.py::test_geometry_K PASSED [ 32%]
tests/test_Geometry.py::test_geometry_L PASSED [ 35%]
tests/test_Geometry.py::test_geometry_M PASSED [ 39%]
tests/test_Geometry.py::test_geometry_N PASSED [ 42%]
tests/test_Geometry.py::test_geometry_P PASSED [ 46%]
tests/test_Geometry.py::test_geometry_Q PASSED [ 50%]
tests/test_Geometry.py::test_geometry_R PASSED [ 53%]
tests/test_Geometry.py::test_geometry_S PASSED [ 57%]
tests/test_Geometry.py::test_geometry_T PASSED [ 60%]
tests/test_Geometry.py::test_geometry_V PASSED [ 64%]
tests/test_Geometry.py::test_geometry_W PASSED [ 67%]
tests/test_Geometry.py::test_geometry_Y PASSED [ 71%]
tests/test_PeptideBuilder.py::test_add_residue PASSED [ 75%]
tests/test_PeptideBuilder.py::test_add_residue2 PASSED [ 78%]
tests/test_PeptideBuilder.py::test_make_structure_from_geos PASSED [ 82%]
tests/test_PeptideBuilder.py::test_make_extended_structure PASSED [ 85%]
tests/test_PeptideBuilder.py::test_make_structure_from_geos2 PASSED [ 89%]
tests/test_PeptideBuilder.py::test_make_structure PASSED [ 92%]
tests/test_PeptideBuilder.py::test_make_structure2 PASSED [ 96%]
tests/test_PeptideBuilder.py::test_add_terminal_OXT PASSED [100%]
=============================== warnings summary ===============================
tests/test_PeptideBuilder.py: 10 warnings
/usr/lib/python3/dist-packages/Bio/PDB/PDBParser.py:395: PDBConstructionWarning: Ignoring unrecognized record 'TER' at line 168
warnings.warn(
tests/test_PeptideBuilder.py: 10 warnings
/usr/lib/python3/dist-packages/Bio/PDB/PDBParser.py:395: PDBConstructionWarning: Ignoring unrecognized record 'END' at line 169
warnings.warn(
tests/test_PeptideBuilder.py::test_add_terminal_OXT
/usr/lib/python3/dist-packages/Bio/PDB/PDBParser.py:395: PDBConstructionWarning: Ignoring unrecognized record 'END' at line 170
warnings.warn(
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
---------- coverage: platform linux, python 3.11.2-final-0 -----------
Name Stmts Miss Cover
------------------------------------------------------
PeptideBuilder/Geometry.py 846 204 76%
PeptideBuilder/PeptideBuilder.py 869 4 99%
PeptideBuilder/__init__.py 3 0 100%
------------------------------------------------------
TOTAL 1718 208 88%
======================= 28 passed, 21 warnings in 4.42s ========================
make[1]: Leaving directory '/build/reproducible-path/peptidebuilder-1.1.0'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=pybuild
dh_prep -O--buildsystem=pybuild
rm -f -- debian/python3-peptidebuilder.substvars
rm -fr -- debian/.debhelper/generated/python3-peptidebuilder/ debian/python3-peptidebuilder/ debian/tmp/
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/peptidebuilder-1.1.0'
dh_auto_install
install -m0755 -d /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder
pybuild --install -i python{version} -p 3.11 --dest-dir /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder
I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder
running install
/usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
running install_lib
creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr
creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib
creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.11
creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.11/dist-packages
creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.11/dist-packages/PeptideBuilder
copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.11_peptidebuilder/build/PeptideBuilder/__init__.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.11/dist-packages/PeptideBuilder
copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.11_peptidebuilder/build/PeptideBuilder/PeptideBuilder.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.11/dist-packages/PeptideBuilder
copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.11_peptidebuilder/build/PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.11/dist-packages/PeptideBuilder
byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.11/dist-packages/PeptideBuilder/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.11/dist-packages/PeptideBuilder/PeptideBuilder.py to PeptideBuilder.cpython-311.pyc
byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.11/dist-packages/PeptideBuilder/Geometry.py to Geometry.cpython-311.pyc
running install_egg_info
running egg_info
creating PeptideBuilder.egg-info
writing PeptideBuilder.egg-info/PKG-INFO
writing dependency_links to PeptideBuilder.egg-info/dependency_links.txt
writing requirements to PeptideBuilder.egg-info/requires.txt
writing top-level names to PeptideBuilder.egg-info/top_level.txt
writing manifest file 'PeptideBuilder.egg-info/SOURCES.txt'
reading manifest file 'PeptideBuilder.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'PeptideBuilder.egg-info/SOURCES.txt'
Copying PeptideBuilder.egg-info to /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.11/dist-packages/PeptideBuilder-1.1.0.egg-info
Skipping SOURCES.txt
running install_scripts
find debian/python3-peptidebuilder/usr/lib/ -name .coverage -delete
make[1]: Leaving directory '/build/reproducible-path/peptidebuilder-1.1.0'
dh_installdocs -O--buildsystem=pybuild
install -m0755 -d debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder
install -p -m0644 debian/copyright debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder/copyright
dh_installchangelogs -O--buildsystem=pybuild
install -m0755 -d debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder
install -p -m0644 debian/.debhelper/generated/python3-peptidebuilder/dh_installchangelogs.dch.trimmed debian/python3-peptidebuilder/usr/share/doc/python3-peptidebuilder/changelog.Debian
dh_python3 -O--buildsystem=pybuild
D: dh_python3 dh_python3:179: version: 5.20230130+deb12u1
D: dh_python3 dh_python3:180: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild']
D: dh_python3 dh_python3:181: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild'])
D: dh_python3 dh_python3:182: supported Python versions: 3.11 (default=3.11)
D: dh_python3 debhelper:183: source=peptidebuilder, binary packages=['python3-peptidebuilder']
D: dh_python3 dh_python3:204: processing package python3-peptidebuilder...
D: dh_python3 fs:52: moving files from debian/python3-peptidebuilder/usr/lib/python3.11/dist-packages to debian/python3-peptidebuilder/usr/lib/python3/dist-packages/
D: dh_python3 fs:400: package python3-peptidebuilder details = {'requires.txt': {'debian/python3-peptidebuilder/usr/lib/python3/dist-packages/PeptideBuilder-1.1.0.egg-info/requires.txt'}, 'egg-info': set(), 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': set(), 'ext_no_version': set()}
D: dh_python3 depends:117: generating dependencies for package python3-peptidebuilder
D: dh_python3 pydist:173: trying to find dependency for Biopython (python=None)
D: dh_python3 pydist:207: dependency: module seems to be installed
D: dh_python3 pydist:270: dependency: included in build-deps
D: dh_python3 depends:281: D={'python3:any', 'python3-biopython'}; R=[]; S=[]; E=[], B=[]; RT=[]
dh_installsystemduser -O--buildsystem=pybuild
dh_perl -O--buildsystem=pybuild
dh_link -O--buildsystem=pybuild
dh_strip_nondeterminism -O--buildsystem=pybuild
dh_compress -O--buildsystem=pybuild
cd debian/python3-peptidebuilder
chmod a-x usr/share/doc/python3-peptidebuilder/changelog.Debian
gzip -9nf usr/share/doc/python3-peptidebuilder/changelog.Debian
cd '/build/reproducible-path/peptidebuilder-1.1.0'
dh_fixperms -O--buildsystem=pybuild
find debian/python3-peptidebuilder ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/python3-peptidebuilder/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-peptidebuilder/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/python3-peptidebuilder/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/python3-peptidebuilder -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/python3-peptidebuilder/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w
dh_missing -O--buildsystem=pybuild
dh_installdeb -O--buildsystem=pybuild
install -m0755 -d debian/python3-peptidebuilder/DEBIAN
printf '#!/bin/sh\nset -e\n' > debian/python3-peptidebuilder/DEBIAN/postinst
cat debian/python3-peptidebuilder.postinst.debhelper >> debian/python3-peptidebuilder/DEBIAN/postinst
chmod 0755 -- debian/python3-peptidebuilder/DEBIAN/postinst
printf '#!/bin/sh\nset -e\n' > debian/python3-peptidebuilder/DEBIAN/prerm
cat debian/python3-peptidebuilder.prerm.debhelper >> debian/python3-peptidebuilder/DEBIAN/prerm
chmod 0755 -- debian/python3-peptidebuilder/DEBIAN/prerm
dh_gencontrol -O--buildsystem=pybuild
install -m0755 -d debian/python3-peptidebuilder/DEBIAN
echo misc:Depends= >> debian/python3-peptidebuilder.substvars
echo misc:Pre-Depends= >> debian/python3-peptidebuilder.substvars
dpkg-gencontrol -ppython3-peptidebuilder -ldebian/changelog -Tdebian/python3-peptidebuilder.substvars -Pdebian/python3-peptidebuilder
chmod 0644 -- debian/python3-peptidebuilder/DEBIAN/control
dh_md5sums -O--buildsystem=pybuild
install -m0755 -d debian/python3-peptidebuilder/DEBIAN
cd debian/python3-peptidebuilder >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/python3-peptidebuilder/DEBIAN/md5sums
dh_builddeb -O--buildsystem=pybuild
dpkg-deb --root-owner-group --build debian/python3-peptidebuilder ..
dpkg-deb: building package 'python3-peptidebuilder' in '../python3-peptidebuilder_1.1.0-3_all.deb'.
dpkg-genbuildinfo --build=binary -O../peptidebuilder_1.1.0-3_i386.buildinfo
dpkg-genchanges --build=binary -O../peptidebuilder_1.1.0-3_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-source: info: using options from peptidebuilder-1.1.0/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
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/12488 and its subdirectories
I: Current time: Sun Jan 7 04:27:59 -12 2024
I: pbuilder-time-stamp: 1704644879
Sun Jan 7 16:28:00 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos16-i386.debian.net.
Sun Jan 7 16:28:00 UTC 2024 I: Preparing to do remote build '2' on ionos16-i386.debian.net.
Sun Jan 7 16:29:11 UTC 2024 I: Deleting $TMPDIR on ionos16-i386.debian.net.
Sun Jan 7 16:29:11 UTC 2024 I: peptidebuilder_1.1.0-3_i386.changes:
Format: 1.8
Date: Fri, 08 Oct 2021 22:50:43 +0200
Source: peptidebuilder
Binary: python3-peptidebuilder
Architecture: all
Version: 1.1.0-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
python3-peptidebuilder - generate atomic oligopeptide 3D structure from sequence
Changes:
peptidebuilder (1.1.0-3) unstable; urgency=medium
.
* Team upload.
* Upstream has broken semantic versioning - so mangle upstream version
to really get the latest upstream code
* Standards-Version: 4.6.0 (routine-update)
Checksums-Sha1:
2568e0bbbe1b6c697aeadb71f2fa32913e892d0f 7322 peptidebuilder_1.1.0-3_i386.buildinfo
743bdee8020530d47ac5378a395a73d7ea7e842a 12728 python3-peptidebuilder_1.1.0-3_all.deb
Checksums-Sha256:
2976acf3df7da18a4779d6776acca463add62c9bfea23cc0e0b09320b2e703f8 7322 peptidebuilder_1.1.0-3_i386.buildinfo
76e7386e692d3bbc8639240f22cb181dd18aed421227e8e95fb2c0d01e150cf9 12728 python3-peptidebuilder_1.1.0-3_all.deb
Files:
5c4eea38f1d5cf5464c89a15aeb8497e 7322 science optional peptidebuilder_1.1.0-3_i386.buildinfo
643797f3c3d9120237e9637f2f8c8fc1 12728 science optional python3-peptidebuilder_1.1.0-3_all.deb
Sun Jan 7 16:29:12 UTC 2024 I: diffoscope 240 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.XB5lODhk/peptidebuilder_1.1.0-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.XB5lODhk/peptidebuilder_1.1.0-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.XB5lODhk/peptidebuilder_1.1.0-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.XB5lODhk/b1/peptidebuilder_1.1.0-3_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.XB5lODhk/b2/peptidebuilder_1.1.0-3_i386.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: 0.017s)
0.017s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Sun Jan 7 16:29:13 UTC 2024 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists.
Sun Jan 7 16:29:13 UTC 2024 I: peptidebuilder from bookworm built successfully and reproducibly on i386.
Sun Jan 7 16:29:15 UTC 2024 I: Submitting .buildinfo files to external archives:
Sun Jan 7 16:29:15 UTC 2024 I: Submitting 12K b1/peptidebuilder_1.1.0-3_i386.buildinfo.asc
Sun Jan 7 16:29:17 UTC 2024 I: Submitting 12K b2/peptidebuilder_1.1.0-3_i386.buildinfo.asc
Sun Jan 7 16:29:17 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Jan 7 16:29:17 UTC 2024 I: Done submitting .buildinfo files.
Sun Jan 7 16:29:17 UTC 2024 I: Removing signed peptidebuilder_1.1.0-3_i386.buildinfo.asc files:
removed './b1/peptidebuilder_1.1.0-3_i386.buildinfo.asc'
removed './b2/peptidebuilder_1.1.0-3_i386.buildinfo.asc'