I: pbuilder: network access will be disabled during build
I: Current time: Fri Apr 10 17:12:39 +14 2026
I: pbuilder-time-stamp: 1775790759
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [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
dpkg-source: warning: cannot verify inline signature for ./peptidebuilder_1.1.0-3.dsc: unsupported subcommand
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/723472/tmp/hooks/D01_modify_environment starting
debug: Running on ionos15-amd64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Apr 10 03:12 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/723472/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/723472/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=amd64
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
DIRSTACK=()
DISTRIBUTION=unstable
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=x86_64
HOST_ARCH=amd64
IFS='
'
INVOCATION_ID=1321169b4cb34a2ab03d9fa8be73dc86
LANG=C
LANGUAGE=et_EE:et
LC_ALL=C
MACHTYPE=x86_64-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=723472
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.M4HzYKbm/pbuilderrc_JmCs --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.M4HzYKbm/b2 --logfile b2/build.log peptidebuilder_1.1.0-3.dsc'
SUDO_GID=111
SUDO_UID=106
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://213.165.73.152:3128
I: uname -a
Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/723472/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), 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 ... 19783 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on 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} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{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} libmagic1t64{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libtiff6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-autocommand{a} python3-biopython{a} python3-cairo{a} python3-chardet{a} python3-coverage{a} python3-freetype{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-pytest{a} python3-pytest-cov{a} python3-reportlab{a} python3-rlpycairo{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{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 fonts-dejavu-extra 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, 124 newly installed, 0 to remove and 0 not upgraded.
Need to get 63.3 MB of archives. After unpacking 221 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 12.0.0 [28.9 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.2-2 [28.1 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-4 [139 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.3+ds-4 [5085 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-7 [294 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 42 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250306 [115 kB]
Get: 52 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB]
Get: 55 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.47-1 [282 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+24 [217 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB]
Get: 62 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB]
Get: 64 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get: 66 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get: 67 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get: 68 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get: 70 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB]
Get: 71 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB]
Get: 73 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB]
Get: 74 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB]
Get: 75 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get: 76 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.83.5-1 [1513 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB]
Get: 82 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB]
Get: 83 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 84 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-hotkeys all 0.2.0-1 [12.6 kB]
Get: 85 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B]
Get: 86 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-metadata all 12-4 [6532 B]
Get: 87 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [184 kB]
Get: 88 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB]
Get: 89 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB]
Get: 90 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB]
Get: 91 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-1 [204 kB]
Get: 92 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB]
Get: 93 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB]
Get: 94 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB]
Get: 95 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB]
Get: 96 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB]
Get: 97 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB]
Get: 98 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.2-2 [1044 B]
Get: 99 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 100 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get: 101 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.1.0-5+b1 [513 kB]
Get: 102 http://deb.debian.org/debian unstable/main amd64 python3-cairo amd64 1.26.1-2+b2 [114 kB]
Get: 103 http://deb.debian.org/debian unstable/main amd64 python3-freetype all 2.5.1-1 [89.3 kB]
Get: 104 http://deb.debian.org/debian unstable/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B]
Get: 105 http://deb.debian.org/debian unstable/main amd64 python3-reportlab all 4.3.1-1 [1158 kB]
Get: 106 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB]
Get: 107 http://deb.debian.org/debian unstable/main amd64 w3c-sgml-lib all 1.3-3 [273 kB]
Get: 108 http://deb.debian.org/debian unstable/main amd64 python3-biopython amd64 1.85+dfsg-2+b1 [1672 kB]
Get: 109 http://deb.debian.org/debian unstable/main amd64 python3-coverage amd64 7.6.0+dfsg1-2+b2 [175 kB]
Get: 110 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 111 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 112 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB]
Get: 113 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 114 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B]
Get: 115 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 116 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB]
Get: 117 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 118 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 119 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.8.0-1 [724 kB]
Get: 120 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B]
Get: 121 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB]
Get: 122 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB]
Get: 123 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.4-1 [250 kB]
Get: 124 http://deb.debian.org/debian unstable/main amd64 python3-pytest-cov all 5.0.0-1 [26.8 kB]
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Unpacking python3-autocommand (2.2.2-3) ...
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Unpacking python3-chardet (5.2.0+dfsg-2) ...
Selecting previously unselected package python3-pil:amd64.
Preparing to unpack .../087-python3-pil_11.1.0-5+b1_amd64.deb ...
Unpacking python3-pil:amd64 (11.1.0-5+b1) ...
Selecting previously unselected package python3-cairo.
Preparing to unpack .../088-python3-cairo_1.26.1-2+b2_amd64.deb ...
Unpacking python3-cairo (1.26.1-2+b2) ...
Selecting previously unselected package python3-freetype.
Preparing to unpack .../089-python3-freetype_2.5.1-1_all.deb ...
Unpacking python3-freetype (2.5.1-1) ...
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Unpacking python3-rlpycairo (0.3.0-3) ...
Selecting previously unselected package python3-reportlab.
Preparing to unpack .../091-python3-reportlab_4.3.1-1_all.deb ...
Unpacking python3-reportlab (4.3.1-1) ...
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Unpacking w3c-sgml-lib (1.3-3) ...
Selecting previously unselected package python3-biopython.
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Unpacking python3-biopython (1.85+dfsg-2+b1) ...
Selecting previously unselected package python3-coverage.
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Unpacking python3-coverage (7.6.0+dfsg1-2+b2) ...
Selecting previously unselected package python3-more-itertools.
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Selecting previously unselected package python3-typing-extensions.
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Unpacking python3-typing-extensions (4.12.2-2) ...
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Unpacking python3-inflect (7.3.1-2) ...
Selecting previously unselected package python3-iniconfig.
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Unpacking python3-iniconfig (1.1.1-2) ...
Selecting previously unselected package python3-jaraco.functools.
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Unpacking python3-zipp (3.21.0-1) ...
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Selecting previously unselected package python3-pytest.
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Unpacking python3-pytest (8.3.4-1) ...
Selecting previously unselected package python3-pytest-cov.
Preparing to unpack .../110-python3-pytest-cov_5.0.0-1_all.deb ...
Unpacking python3-pytest-cov (5.0.0-1) ...
Setting up media-types (12.0.0) ...
Setting up libpipeline1:amd64 (1.5.8-1) ...
Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ...
Setting up liblcms2-2:amd64 (2.16-2) ...
Setting up libpixman-1-0:amd64 (0.44.0-3) ...
Setting up libsharpyuv0:amd64 (1.5.0-0.1) ...
Setting up libxau6:amd64 (1:1.0.11-1) ...
Setting up libxdmcp6:amd64 (1:1.1.5-1) ...
Setting up libxcb1:amd64 (1.17.0-2+b1) ...
Setting up libicu72:amd64 (72.1-6) ...
Setting up liblerc4:amd64 (4.0.0+ds-5) ...
Setting up bsdextrautils (2.40.4-5) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libxcb-render0:amd64 (1.17.0-2+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.24.1) ...
Setting up libbrotli1:amd64 (1.1.0-2+b7) ...
Setting up libmagic1t64:amd64 (1:5.45-3+b1) ...
Setting up x11-common (1:7.7+24) ...
invoke-rc.d: could not determine current runlevel
Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix.
Setting up libdeflate0:amd64 (1.23-1+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-7) ...
Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ...
Setting up file (1:5.45-3+b1) ...
Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ...
Setting up libjbig0:amd64 (2.1-6.1+b2) ...
Setting up libelf1t64:amd64 (0.192-4) ...
Setting up tzdata (2025a-2) ...
Current default time zone: 'Etc/UTC'
Local time is now: Fri Apr 10 03:13:37 UTC 2026.
Universal Time is now: Fri Apr 10 03:13:37 UTC 2026.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ...
Setting up autotools-dev (20220109.1) ...
Setting up libblas3:amd64 (3.12.1-2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
Setting up libjpeg62-turbo:amd64 (1:2.1.5-3.1) ...
Setting up libx11-data (2:1.8.10-2) ...
Setting up xfonts-encodings (1:1.0.4-2.2) ...
Setting up libfribidi0:amd64 (1.0.16-1) ...
Setting up libimagequant0:amd64 (2.18.0-1+b2) ...
Setting up libunistring5:amd64 (1.3-1) ...
Setting up fonts-dejavu-mono (2.37-8) ...
Setting up libpng16-16t64:amd64 (1.6.47-1) ...
Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-4) ...
Setting up autopoint (0.23.1-1) ...
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libgfortran5:amd64 (14.2.0-17) ...
Setting up autoconf (2.72-3) ...
Setting up libwebp7:amd64 (1.5.0-0.1) ...
Setting up libffi8:amd64 (3.4.7-1) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libtiff6:amd64 (4.5.1+git230720-5) ...
Setting up libuchardet0:amd64 (0.0.8-1+b2) ...
Setting up libopenjp2-7:amd64 (2.5.3-1) ...
Setting up libx11-6:amd64 (2:1.8.10-2) ...
Setting up netbase (6.4) ...
Setting up sgml-base (1.31) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libjs-jquery-hotkeys (0.2.0-1) ...
Setting up libwebpmux3:amd64 (1.5.0-0.1) ...
Setting up readline-common (8.2-6) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up liblapack3:amd64 (3.12.1-2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
Setting up gettext (0.23.1-1) ...
Setting up libxrender1:amd64 (1:0.9.10-1.1+b4) ...
Setting up libtool (2.5.4-4) ...
Setting up fontconfig-config (2.15.0-2) ...
Setting up libwebpdemux2:amd64 (1.5.0-0.1) ...
Setting up libxext6:amd64 (2:1.3.4-1+b3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libglib2.0-0t64:amd64 (2.83.5-1) ...
No schema files found: doing nothing.
Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ...
Setting up libjs-jquery-metadata (12-4) ...
Setting up libjs-jquery-isonscreen (1.2.0-1.1) ...
Setting up libreadline8t64:amd64 (8.2-6) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ...
Setting up groff-base (1.23.0-7) ...
Setting up xml-core (0.19) ...
Setting up libharfbuzz0b:amd64 (10.2.0-1) ...
Setting up libfontconfig1:amd64 (2.15.0-2) ...
Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ...
Setting up libpython3-stdlib:amd64 (3.13.2-2) ...
Setting up python3.13 (3.13.2-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up python3 (3.13.2-2) ...
Setting up python3-zipp (3.21.0-1) ...
Setting up python3-freetype (2.5.1-1) ...
Setting up xfonts-utils (1:7.7+7) ...
Setting up python3-autocommand (2.2.2-3) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libcairo2:amd64 (1.18.2-2) ...
Setting up python3-packaging (24.2-1) ...
Setting up python3-chardet (5.2.0+dfsg-2) ...
Setting up libraqm0:amd64 (0.10.2-1) ...
Setting up python3-typing-extensions (4.12.2-2) ...
Setting up python3-numpy (1:2.2.3+ds-4) ...
Setting up python3-pluggy (1.5.0-1) ...
Setting up dh-python (6.20250306) ...
Setting up python3-more-itertools (10.6.0-1) ...
Setting up python3-iniconfig (1.1.1-2) ...
Setting up python3-cairo (1.26.1-2+b2) ...
Setting up python3-jaraco.functools (4.1.0-1) ...
Setting up python3-jaraco.context (6.0.1-1) ...
Setting up python3-pytest (8.3.4-1) ...
Setting up python3-typeguard (4.4.2-1) ...
Setting up python3-all (3.13.2-2) ...
Setting up python3-coverage (7.6.0+dfsg1-2+b2) ...
Setting up debhelper (13.24.1) ...
Setting up python3-pytest-cov (5.0.0-1) ...
Setting up fonts-urw-base35 (20200910-8) ...
Setting up python3-pil:amd64 (11.1.0-5+b1) ...
Setting up python3-inflect (7.3.1-2) ...
Setting up python3-rlpycairo (0.3.0-3) ...
Setting up python3-jaraco.text (4.0.0-1) ...
Setting up python3-reportlab (4.3.1-1) ...
Setting up python3-pkg-resources (75.8.0-1) ...
Setting up python3-setuptools (75.8.0-1) ...
Processing triggers for libc-bin (2.41-3) ...
Processing triggers for sgml-base (1.31) ...
Setting up w3c-sgml-lib (1.3-3) ...
Setting up python3-biopython (1.85+dfsg-2+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: user script /srv/workspace/pbuilder/723472/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/723472/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/peptidebuilder-1.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 amd64
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 3.13
I: pybuild base:311: python3.13 setup.py clean
running clean
removing '/build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build' (and everything under it)
'build/bdist.linux-x86_64' does not exist -- can't clean it
'build/scripts-3.13' 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 \( -name autom4te.cache -o -name __pycache__ \) -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 3.13
I: pybuild base:311: python3.13 setup.py config
running config
dh_auto_build -O--buildsystem=pybuild
pybuild --build -i python{version} -p 3.13
I: pybuild base:311: /usr/bin/python3 setup.py build
running build
running build_py
creating /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder
copying PeptideBuilder/PeptideBuilder.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder
copying PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder
copying PeptideBuilder/__init__.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_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 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3
cachedir: .pytest_cache
rootdir: /build/reproducible-path/peptidebuilder-1.1.0
configfile: pytest.ini
testpaths: tests
plugins: cov-5.0.0, typeguard-4.4.2
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:384: 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:384: 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:384: 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 3.13.2-final-0 -----------
Name Stmts Miss Cover
------------------------------------------------------
PeptideBuilder/Geometry.py 846 204 76%
PeptideBuilder/PeptideBuilder.py 869 3 99%
PeptideBuilder/__init__.py 3 0 100%
------------------------------------------------------
TOTAL 1718 207 88%
======================= 28 passed, 21 warnings in 1.98s ========================
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 3.13 --dest-dir=/build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder
I: pybuild base:311: /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/_distutils/cmd.py:79: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` directly.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
********************************************************************************
!!
self.initialize_options()
running build
running build_py
running install_lib
creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages
creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder
copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/PeptideBuilder.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder
copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder
copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.13_peptidebuilder/build/PeptideBuilder/__init__.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder
byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/PeptideBuilder.py to PeptideBuilder.cpython-313.pyc
byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/Geometry.py to Geometry.cpython-313.pyc
byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages/PeptideBuilder/__init__.py to __init__.cpython-313.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/python3.13/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_python3:180: version: 6.20250306
D: dh_python3 dh_python3:181: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild']
D: dh_python3 dh_python3:182: 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_python3:183: supported Python versions: 3.13 (default=3.13)
D: dh_python3 debhelper:174: source=peptidebuilder, binary packages=['python3-peptidebuilder']
D: dh_python3 dh_python3:205: processing package python3-peptidebuilder...
D: dh_python3 fs:50: moving files from debian/python3-peptidebuilder/usr/lib/python3.13/dist-packages to debian/python3-peptidebuilder/usr/lib/python3/dist-packages/
D: dh_python3 fs:338: package python3-peptidebuilder details = {'requires.txt': {'debian/python3-peptidebuilder/usr/lib/python3/dist-packages/PeptideBuilder-1.1.0.egg-info/requires.txt'}, 'egg-info': {'debian/python3-peptidebuilder/usr/lib/python3/dist-packages/PeptideBuilder-1.1.0.egg-info/PKG-INFO'}, '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:103: generating dependencies for package python3-peptidebuilder
D: dh_python3 pydist:175: trying to find dependency for Biopython (python=None)
D: dh_python3 pydist:209: dependency: module seems to be installed
D: dh_python3 pydist:284: dependency: included in build-deps
D: dh_python3 depends:253: D={'python3-biopython', 'python3:any'}; 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 -cdebian/control -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_amd64.buildinfo
dpkg-genchanges --build=binary -O../peptidebuilder_1.1.0-3_amd64.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: user script /srv/workspace/pbuilder/723472/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/723472/tmp/hooks/B01_cleanup finished
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/723472 and its subdirectories
I: Current time: Fri Apr 10 17:14:50 +14 2026
I: pbuilder-time-stamp: 1775790890