I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 27 13:37:40 +14 2024 I: pbuilder-time-stamp: 1714174660 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 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/2805/tmp/hooks/D01_modify_environment starting debug: Running on virt64z. 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 26 23:37 /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/2805/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2805/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]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=70f5bcab5b314025954d7e5088e46059 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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=2805 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.gLUNa9Zd/pbuilderrc_RlF5 --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.gLUNa9Zd/b2 --logfile b2/build.log peptidebuilder_1.1.0-3.dsc' SUDO_GID=110 SUDO_UID=103 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 25 07:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2805/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team 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 ... 19440 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} libbsd0{a} libcairo2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{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} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libsub-override-perl{a} libtiff6{a} libtool{a} libuchardet0{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-biopython{a} python3-cairo{a} python3-chardet{a} python3-coverage{a} python3-distutils{a} python3-freetype{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{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} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-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, 120 newly installed, 0 to remove and 0 not upgraded. Need to get 63.5 MB of archives. After unpacking 209 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf libpython3.11-minimal armhf 3.11.9-1 [805 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf python3.11-minimal armhf 3.11.9-1 [1600 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf python3-minimal armhf 3.11.8-1 [26.3 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf tzdata all 2024a-3 [255 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf readline-common all 8.2-4 [69.3 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf libreadline8t64 armhf 8.2-4 [145 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf libpython3.11-stdlib armhf 3.11.9-1 [1704 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf python3.11 armhf 3.11.9-1 [602 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf libpython3-stdlib armhf 3.11.8-1 [9332 B] Get: 15 http://deb.debian.org/debian unstable/main armhf python3 armhf 3.11.8-1 [27.4 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf libpython3.12-minimal armhf 3.12.3-1 [795 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf python3.12-minimal armhf 3.12.3-1 [1783 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf sgml-base all 1.31 [15.4 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-3+b1 [1091 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40-7 [85.6 kB] Get: 27 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.12.1-1 [1375 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf autoconf all 2.71-3 [332 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf autopoint all 0.21-14 [496 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-7 [517 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 38 http://deb.debian.org/debian unstable/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 41 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.191-1+b1 [183 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf debhelper all 13.15.3 [901 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf python3-pkg-resources all 68.1.2-2 [241 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf python3-distutils all 3.12.3-1 [131 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf python3-setuptools all 68.1.2-2 [468 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf dh-python all 6.20240422 [107 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf fonts-dejavu-mono all 2.37-8 [489 kB] Get: 55 http://deb.debian.org/debian unstable/main armhf fonts-dejavu-core all 2.37-8 [840 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf libfontenc1 armhf 1:1.1.8-1 [20.6 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf libpng16-16t64 armhf 1.6.43-5 [262 kB] Get: 59 http://deb.debian.org/debian unstable/main armhf libfreetype6 armhf 2.13.2+dfsg-1+b4 [372 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf x11-common all 1:7.7+23 [252 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 62 http://deb.debian.org/debian unstable/main armhf xfonts-utils armhf 1:7.7+6 [84.5 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 64 http://deb.debian.org/debian unstable/main armhf fontconfig-config armhf 2.15.0-1.1 [317 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf libblas3 armhf 3.12.0-3 [108 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf libbsd0 armhf 0.12.2-1 [127 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf libfontconfig1 armhf 2.15.0-1.1 [370 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf libpixman-1-0 armhf 0.42.2-1+b1 [476 kB] Get: 69 http://deb.debian.org/debian unstable/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 70 http://deb.debian.org/debian unstable/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 71 http://deb.debian.org/debian unstable/main armhf libxcb1 armhf 1.17.0-1 [140 kB] Get: 72 http://deb.debian.org/debian unstable/main armhf libx11-data all 2:1.8.7-1 [328 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf libx11-6 armhf 2:1.8.7-1 [735 kB] Get: 74 http://deb.debian.org/debian unstable/main armhf libxcb-render0 armhf 1.17.0-1 [114 kB] Get: 75 http://deb.debian.org/debian unstable/main armhf libxcb-shm0 armhf 1.17.0-1 [105 kB] Get: 76 http://deb.debian.org/debian unstable/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 77 http://deb.debian.org/debian unstable/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.1 kB] Get: 78 http://deb.debian.org/debian unstable/main armhf libcairo2 armhf 1.18.0-3+b1 [442 kB] Get: 79 http://deb.debian.org/debian unstable/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 80 http://deb.debian.org/debian unstable/main armhf libfribidi0 armhf 1.0.13-3+b1 [69.4 kB] Get: 81 http://deb.debian.org/debian unstable/main armhf libgfortran5 armhf 14-20240330-1 [264 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf libglib2.0-0t64 armhf 2.78.4-7 [1285 kB] Get: 83 http://deb.debian.org/debian unstable/main armhf libgraphite2-3 armhf 1.3.14-2 [63.2 kB] Get: 84 http://deb.debian.org/debian unstable/main armhf libharfbuzz0b armhf 8.3.0-2+b1 [2156 kB] Get: 85 http://deb.debian.org/debian unstable/main armhf libimagequant0 armhf 2.18.0-1 [30.4 kB] Get: 86 http://deb.debian.org/debian unstable/main armhf libjbig0 armhf 2.1-6.1+b1 [27.3 kB] Get: 87 http://deb.debian.org/debian unstable/main armhf libjpeg62-turbo armhf 1:2.1.5-3 [143 kB] Get: 88 http://deb.debian.org/debian unstable/main armhf libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B] Get: 89 http://deb.debian.org/debian unstable/main armhf libjs-jquery-metadata all 12-4 [6532 B] Get: 90 http://deb.debian.org/debian unstable/main armhf libjs-jquery-tablesorter all 1:2.31.3+dfsg1-3 [184 kB] Get: 91 http://deb.debian.org/debian unstable/main armhf libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB] Get: 92 http://deb.debian.org/debian unstable/main armhf liblapack3 armhf 3.12.0-3 [1803 kB] Get: 93 http://deb.debian.org/debian unstable/main armhf liblcms2-2 armhf 2.14-2+b1 [126 kB] Get: 94 http://deb.debian.org/debian unstable/main armhf liblerc4 armhf 4.0.0+ds-4+b1 [137 kB] Get: 95 http://deb.debian.org/debian unstable/main armhf libopenjp2-7 armhf 2.5.0-2+b3 [170 kB] Get: 96 http://deb.debian.org/debian unstable/main armhf libpython3.12-stdlib armhf 3.12.3-1 [1808 kB] Get: 97 http://deb.debian.org/debian unstable/main armhf libraqm0 armhf 0.10.1-1+b1 [11.8 kB] Get: 98 http://deb.debian.org/debian unstable/main armhf libsharpyuv0 armhf 1.3.2-0.4+b1 [106 kB] Get: 99 http://deb.debian.org/debian unstable/main armhf libwebp7 armhf 1.3.2-0.4+b1 [262 kB] Get: 100 http://deb.debian.org/debian unstable/main armhf libtiff6 armhf 4.5.1+git230720-4 [301 kB] Get: 101 http://deb.debian.org/debian unstable/main armhf libwebpdemux2 armhf 1.3.2-0.4+b1 [107 kB] Get: 102 http://deb.debian.org/debian unstable/main armhf libwebpmux3 armhf 1.3.2-0.4+b1 [116 kB] Get: 103 http://deb.debian.org/debian unstable/main armhf python3.12 armhf 3.12.3-1 [659 kB] Get: 104 http://deb.debian.org/debian unstable/main armhf python3-all armhf 3.11.8-1 [1056 B] Get: 105 http://deb.debian.org/debian unstable/main armhf python3-numpy armhf 1:1.26.4+ds-8 [4132 kB] Get: 106 http://deb.debian.org/debian unstable/main armhf python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 107 http://deb.debian.org/debian unstable/main armhf python3-pil armhf 10.3.0-2 [521 kB] Get: 108 http://deb.debian.org/debian unstable/main armhf python3-cairo armhf 1.26.0-1 [130 kB] Get: 109 http://deb.debian.org/debian unstable/main armhf python3-freetype all 2.4.0-1 [80.3 kB] Get: 110 http://deb.debian.org/debian unstable/main armhf python3-rlpycairo all 0.3.0-3 [9904 B] Get: 111 http://deb.debian.org/debian unstable/main armhf python3-reportlab all 4.2.0-1 [1149 kB] Get: 112 http://deb.debian.org/debian unstable/main armhf xml-core all 0.19 [20.1 kB] Get: 113 http://deb.debian.org/debian unstable/main armhf w3c-sgml-lib all 1.3-3 [273 kB] Get: 114 http://deb.debian.org/debian unstable/main armhf python3-biopython armhf 1.83+dfsg1-2 [1601 kB] Get: 115 http://deb.debian.org/debian unstable/main armhf python3-coverage armhf 7.2.7+dfsg1-1+b1 [168 kB] Get: 116 http://deb.debian.org/debian unstable/main armhf python3-iniconfig all 1.1.1-2 [6396 B] Get: 117 http://deb.debian.org/debian unstable/main armhf python3-packaging all 24.0-1 [45.5 kB] Get: 118 http://deb.debian.org/debian unstable/main armhf python3-pluggy all 1.5.0-1 [26.9 kB] Get: 119 http://deb.debian.org/debian unstable/main armhf python3-pytest all 8.1.1-2 [245 kB] Get: 120 http://deb.debian.org/debian unstable/main armhf python3-pytest-cov all 4.1.0-1 [26.7 kB] Fetched 63.5 MB in 2s (36.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libjs-jquery. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19440 files and directories currently installed.) Preparing to unpack .../libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-hotkeys. Preparing to unpack .../libjs-jquery-hotkeys_0~20130707+git2d51e3a9+dfsg-2.1_all.deb ... Unpacking libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... Selecting previously unselected package libpython3.11-minimal:armhf. Preparing to unpack .../libpython3.11-minimal_3.11.9-1_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.9-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.2-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_armhf.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:armhf (3.11.9-1) ... Setting up libexpat1:armhf (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 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Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_armhf.deb ... Unpacking python3.11 (3.11.9-1) ... 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Selecting previously unselected package libpython3.12-minimal:armhf. Preparing to unpack .../001-libpython3.12-minimal_3.12.3-1_armhf.deb ... Unpacking libpython3.12-minimal:armhf (3.12.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.3-1_armhf.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../003-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3) ... 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Unpacking libsharpyuv0:armhf (1.3.2-0.4+b1) ... Selecting previously unselected package libwebp7:armhf. Preparing to unpack .../084-libwebp7_1.3.2-0.4+b1_armhf.deb ... Unpacking libwebp7:armhf (1.3.2-0.4+b1) ... Selecting previously unselected package libtiff6:armhf. Preparing to unpack .../085-libtiff6_4.5.1+git230720-4_armhf.deb ... Unpacking libtiff6:armhf (4.5.1+git230720-4) ... Selecting previously unselected package libwebpdemux2:armhf. Preparing to unpack .../086-libwebpdemux2_1.3.2-0.4+b1_armhf.deb ... Unpacking libwebpdemux2:armhf (1.3.2-0.4+b1) ... Selecting previously unselected package libwebpmux3:armhf. Preparing to unpack .../087-libwebpmux3_1.3.2-0.4+b1_armhf.deb ... Unpacking libwebpmux3:armhf (1.3.2-0.4+b1) ... Selecting previously unselected package python3.12. Preparing to unpack .../088-python3.12_3.12.3-1_armhf.deb ... Unpacking python3.12 (3.12.3-1) ... Selecting previously unselected package python3-all. 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Preparing to unpack .../095-python3-rlpycairo_0.3.0-3_all.deb ... Unpacking python3-rlpycairo (0.3.0-3) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../096-python3-reportlab_4.2.0-1_all.deb ... Unpacking python3-reportlab (4.2.0-1) ... Selecting previously unselected package xml-core. Preparing to unpack .../097-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package w3c-sgml-lib. Preparing to unpack .../098-w3c-sgml-lib_1.3-3_all.deb ... Unpacking w3c-sgml-lib (1.3-3) ... Selecting previously unselected package python3-biopython. Preparing to unpack .../099-python3-biopython_1.83+dfsg1-2_armhf.deb ... Unpacking python3-biopython (1.83+dfsg1-2) ... Selecting previously unselected package python3-coverage. Preparing to unpack .../100-python3-coverage_7.2.7+dfsg1-1+b1_armhf.deb ... Unpacking python3-coverage (7.2.7+dfsg1-1+b1) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../101-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../102-python3-packaging_24.0-1_all.deb ... Unpacking python3-packaging (24.0-1) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../103-python3-pluggy_1.5.0-1_all.deb ... Unpacking python3-pluggy (1.5.0-1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../104-python3-pytest_8.1.1-2_all.deb ... Unpacking python3-pytest (8.1.1-2) ... Selecting previously unselected package python3-pytest-cov. Preparing to unpack .../105-python3-pytest-cov_4.1.0-1_all.deb ... Unpacking python3-pytest-cov (4.1.0-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up libgraphite2-3:armhf (1.3.14-2) ... Setting up liblcms2-2:armhf (2.14-2+b1) ... Setting up libpixman-1-0:armhf (0.42.2-1+b1) ... Setting up libsharpyuv0:armhf (1.3.2-0.4+b1) ... Setting up libxau6:armhf (1:1.0.9-1) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up liblerc4:armhf (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.40-7) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:armhf (1.1.0-2+b3) ... Setting up libmagic1t64:armhf (1:5.45-3) ... Setting up libpython3.12-minimal:armhf (3.12.3-1) ... 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 libdeflate0:armhf (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... Setting up libjbig0:armhf (2.1-6.1+b1) ... Setting up libelf1t64:armhf (0.191-1+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Apr 26 23:38:32 UTC 2024. Universal Time is now: Fri Apr 26 23:38:32 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:armhf (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:armhf (2.78.4-7) ... No schema files found: doing nothing. Setting up libblas3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libjpeg62-turbo:armhf (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:armhf (1.0.13-3+b1) ... Setting up libimagequant0:armhf (2.18.0-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:armhf (1.6.43-5) ... Setting up autopoint (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgfortran5:armhf (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:armhf (1.3.2-0.4+b1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.22) ... Setting up libtiff6:armhf (4.5.1+git230720-4) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libopenjp2-7:armhf (2.5.0-2+b3) ... Setting up libsub-override-perl (0.10-1) ... 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 (0~20130707+git2d51e3a9+dfsg-2.1) ... Setting up libwebpmux3:armhf (1.3.2-0.4+b1) ... Setting up libbsd0:armhf (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b2) ... 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 python3.12-minimal (3.12.3-1) ... Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up liblapack3:armhf (3.12.0-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libxcb1:armhf (1.17.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:armhf (1.17.0-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:armhf (1.3.2-0.4+b1) ... Setting up libxcb-shm0:armhf (1.17.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:armhf (2.13.2+dfsg-1+b4) ... Setting up libjs-jquery-metadata (12-4) ... Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... Setting up libreadline8t64:armhf (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-3) ... Setting up groff-base (1.23.0-3+b1) ... Setting up xml-core (0.19) ... Setting up libx11-6:armhf (2:1.8.7-1) ... Setting up libharfbuzz0b:armhf (8.3.0-2+b1) ... Setting up libfontconfig1:armhf (2.15.0-1.1) ... Setting up libpython3.12-stdlib:armhf (3.12.3-1) ... Setting up libxrender1:armhf (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:armhf (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libxext6:armhf (2:1.3.4-1+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:armhf (1.18.0-3+b1) ... Setting up libraqm0:armhf (0.10.1-1+b1) ... Setting up libpython3-stdlib:armhf (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-freetype (2.4.0-1) ... Setting up python3-pil:armhf (10.3.0-2) ... Setting up python3-packaging (24.0-1) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-cairo (1.26.0-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-pytest (8.1.1-2) ... Setting up python3-all (3.11.8-1) ... Setting up python3-coverage (7.2.7+dfsg1-1+b1) ... Setting up python3-pytest-cov (4.1.0-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-numpy (1:1.26.4+ds-8) ... Setting up python3-reportlab (4.2.0-1) ... Setting up dh-python (6.20240422) ... Processing triggers for libc-bin (2.37-18) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-2) ... 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/2805/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2805/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 dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf 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 "3.12 3.11" I: pybuild base:311: python3.12 setup.py clean running clean removing '/build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.12_peptidebuilder/build' (and everything under it) 'build/bdist.linux-armv7l' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it I: pybuild base:311: 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-armv7l' 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 \( -name autom4te.cache -o -name __pycache__ \) -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 "3.12 3.11" I: pybuild base:311: python3.12 setup.py config running config I: pybuild base:311: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild pybuild --build -i python{version} -p "3.12 3.11" I: pybuild base:311: /usr/bin/python3.12 setup.py build running build running build_py creating /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.12_peptidebuilder/build/PeptideBuilder copying PeptideBuilder/__init__.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.12_peptidebuilder/build/PeptideBuilder copying PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.12_peptidebuilder/build/PeptideBuilder copying PeptideBuilder/PeptideBuilder.py -> /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.12_peptidebuilder/build/PeptideBuilder 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_3.11_peptidebuilder/build/PeptideBuilder copying PeptideBuilder/__init__.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 copying PeptideBuilder/PeptideBuilder.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 3.11.9, pytest-8.1.1, 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-4.1.0 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:388: 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:388: 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:388: 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 3.11.9-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 4.99s ======================== 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 "3.12 3.11" --dest-dir /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder I: pybuild base:311: /usr/bin/python3.12 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:66: 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 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/python3.12 creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.12/dist-packages creating /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.12/dist-packages/PeptideBuilder copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.12_peptidebuilder/build/PeptideBuilder/__init__.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.12/dist-packages/PeptideBuilder copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.12_peptidebuilder/build/PeptideBuilder/Geometry.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.12/dist-packages/PeptideBuilder copying /build/reproducible-path/peptidebuilder-1.1.0/.pybuild/cpython3_3.12_peptidebuilder/build/PeptideBuilder/PeptideBuilder.py -> /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.12/dist-packages/PeptideBuilder byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.12/dist-packages/PeptideBuilder/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.12/dist-packages/PeptideBuilder/Geometry.py to Geometry.cpython-312.pyc byte-compiling /build/reproducible-path/peptidebuilder-1.1.0/debian/python3-peptidebuilder/usr/lib/python3.12/dist-packages/PeptideBuilder/PeptideBuilder.py to PeptideBuilder.cpython-312.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/python3.12/dist-packages/PeptideBuilder-1.1.0.egg-info Skipping SOURCES.txt running install_scripts 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:66: 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/python3.11 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/Geometry.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 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/Geometry.py to Geometry.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 running install_egg_info running 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 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: 6.20240422 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: 3.11,3.12 (default=3.11) D: dh_python3 debhelper:174: source=peptidebuilder, binary packages=['python3-peptidebuilder'] D: dh_python3 dh_python3:204: processing package python3-peptidebuilder... D: dh_python3 fs:50: 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:50: moving files from debian/python3-peptidebuilder/usr/lib/python3.12/dist-packages to debian/python3-peptidebuilder/usr/lib/python3/dist-packages/ D: dh_python3 fs:335: 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: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:253: 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 -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_armhf.buildinfo dpkg-genchanges --build=binary -O../peptidebuilder_1.1.0-3_armhf.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/2805/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2805/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/2805 and its subdirectories I: Current time: Sat Apr 27 13:40:46 +14 2024 I: pbuilder-time-stamp: 1714174846