Running as unit: rb-build-amd64_4-55598.service ==================================================================================== Thu Jun 5 14:44:12 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_4) on jenkins, called using "ionos15-amd64 ionos1-amd64" as arguments. Thu Jun 5 14:44:12 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-M1nxOWEM" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Jun 5 14:44:12 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Jun 5 14:44:12 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-ymlck5' Thu Jun 5 14:44:13 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Thu Jun 5 14:44:13 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-LrkJvW' ok, let's check if python-pdbfixer is building anywhere yet… ok, python-pdbfixer is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of python-pdbfixer in trixie on amd64 on jenkins now. 1st build will be done on ionos15-amd64.debian.net. 2nd build will be done on ionos1-amd64.debian.net. ============================================================================= Thu Jun 5 14:44:33 UTC 2025 I: starting to build python-pdbfixer/trixie/amd64 on jenkins on '2025-06-05 14:44' Thu Jun 5 14:44:33 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_4/55598/console.log 1749134673 amd64 trixie python-pdbfixer Thu Jun 5 14:44:33 UTC 2025 I: Downloading source for trixie/python-pdbfixer=1.9-7 --2025-06-05 14:44:33-- http://deb.debian.org/debian/pool/main/p/python-pdbfixer/python-pdbfixer_1.9-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2196 (2.1K) [text/prs.lines.tag] Saving to: ‘python-pdbfixer_1.9-7.dsc’ 0K .. 100% 255M=0s 2025-06-05 14:44:33 (255 MB/s) - ‘python-pdbfixer_1.9-7.dsc’ saved [2196/2196] --2025-06-05 14:44:33-- http://deb.debian.org/debian/pool/main/p/python-pdbfixer/python-pdbfixer_1.9-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2196 (2.1K) [text/prs.lines.tag] Saving to: ‘python-pdbfixer_1.9-7.dsc’ 0K .. 100% 255M=0s 2025-06-05 14:44:33 (255 MB/s) - ‘python-pdbfixer_1.9-7.dsc’ saved [2196/2196] Thu Jun 5 14:44:33 UTC 2025 I: python-pdbfixer_1.9-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-pdbfixer Binary: python3-pdbfixer Architecture: all Version: 1.9-7 Maintainer: Debian Python Team Uploaders: Andrius Merkys , Homepage: https://github.com/openmm/pdbfixer Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/python-team/packages/python-pdbfixer Vcs-Git: https://salsa.debian.org/python-team/packages/python-pdbfixer.git Testsuite: autopkgtest Testsuite-Triggers: python3-pytest Build-Depends: debhelper-compat (= 13), dh-sequence-python3, help2man, python3, python3-legacy-cgi, python3-openmm, python3-pytest , python3-setuptools, rename Package-List: python3-pdbfixer deb python optional arch=all Checksums-Sha1: 4c91ec5a75bb631f5f90db425c4f609aa61eb75e 648085 python-pdbfixer_1.9.orig.tar.gz ffa8e92b77da6a8ca287c920c2eb722488fe9159 3672 python-pdbfixer_1.9-7.debian.tar.xz Checksums-Sha256: 88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb 648085 python-pdbfixer_1.9.orig.tar.gz e7eb31d789fd5bdaaa13a7dbf0d605b272cd3837580a04b476ed6cf983f3273a 3672 python-pdbfixer_1.9-7.debian.tar.xz Files: 48fc0c9c12eda19e786acbc9e62433f5 648085 python-pdbfixer_1.9.orig.tar.gz 98b259246dba3c210d459ffdca82b92d 3672 python-pdbfixer_1.9-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEEj23hBDd/OxHnQXSHMfMURUShdBoFAmejDEYRHHRjaGV0QGRl Ymlhbi5vcmcACgkQMfMURUShdBpjsg/+OqPiwBoqUp2Lz5Q02+PTtVtKXjF3jG9s mciXDWVEFNkrPdAp/1xcG+gwdB8BmNC+X7cUF213EcnCI8uJzR53HVXDYNEBfmWS 8X6Vek7gYO+CyifoVQcrFzssl8xhBgDfBA2lAAWPvMW1cn835jNLMX7tVpRGyURr f3g57mDqfJnXxIESYyShR6UkZj3uRhVrvwdnoT9+htt1Yf+3ABOhrDvwwFaHpOnI fGB6RqNZO09BlEGVyySmTYx9WBkJ1eddfgNKfRJCFlNh35ByOIHTns3rH3gOUDtP h8SvB1VyQQa5h/v4BEGRM5ogP+MCqNmV0osc7Rfi4ZmBcR7Qc5uSuvhioaJRJgJJ pnwdEa7cobCPYgdiKnP7/bUcuAW4aOVRK3k74zas7gYvK5TwiZbyUqL2UB+TFjK7 wBXTxrrCsyM8r+xcdxddbwlItbc4lX/AxlxtHFJpnAKdd0TNu1E31CkmXoRzPqX5 ZcGJlbypKi/osBYtNfIIFchLUvCzigAglPkmrFvVf8TBmsrigwHw6gWGP+j6GfBo YLzSxZ4UpbasyjgzlwhTOfxcqQMKPFd+ilW9F/y79+KiR4aI6YRrb3RaTqcJplxa mUIVqpibWAcrYsjeASmHDltz7OBSeVZuHyjHHasr7Fv+f7kM7Ep0qt0fUAblhWU/ Inbr5ZqVcU8= =NwpJ -----END PGP SIGNATURE----- Thu Jun 5 14:44:33 UTC 2025 I: Checking whether the package is not for us Thu Jun 5 14:44:33 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Thu Jun 5 14:44:33 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Thu Jun 5 14:44:33 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Jun 5 14:44:33 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-L0PWCb' ==================================================================================== Wed Jul 8 21:07:34 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "1 python-pdbfixer trixie /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS 1.9-7" as arguments. Wed Jul 8 21:07:34 UTC 2026 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-Mhxzqsn6" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Jul 8 21:07:34 UTC 2026 I: Downloading source for trixie/python-pdbfixer=1.9-7 Reading package lists... NOTICE: 'python-pdbfixer' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/python-team/packages/python-pdbfixer.git Please use: git clone https://salsa.debian.org/python-team/packages/python-pdbfixer.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 654 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main python-pdbfixer 1.9-7 (dsc) [2196 B] Get:2 http://deb.debian.org/debian trixie/main python-pdbfixer 1.9-7 (tar) [648 kB] Get:3 http://deb.debian.org/debian trixie/main python-pdbfixer 1.9-7 (diff) [3672 B] Fetched 654 kB in 0s (17.1 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'python-pdbfixer' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/python-team/packages/python-pdbfixer.git Please use: git clone https://salsa.debian.org/python-team/packages/python-pdbfixer.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 654 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main python-pdbfixer 1.9-7 (dsc) [2196 B] Get:2 http://deb.debian.org/debian trixie/main python-pdbfixer 1.9-7 (tar) [648 kB] Get:3 http://deb.debian.org/debian trixie/main python-pdbfixer 1.9-7 (diff) [3672 B] Fetched 654 kB in 0s (17.1 MB/s) Download complete and in download only mode ============================================================================= Building python-pdbfixer in trixie on amd64 on ionos15-amd64 now. Date: Wed Jul 8 21:07:34 UTC 2026 Date UTC: Wed Jul 8 21:07:34 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 8 09:07:34 -12 2026 I: pbuilder-time-stamp: 1783544854 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-pdbfixer_1.9-7.dsc] I: copying [./python-pdbfixer_1.9.orig.tar.gz] I: copying [./python-pdbfixer_1.9-7.debian.tar.xz] I: Extracting source error: the following required arguments were not provided: --keyring Usage: sqv --keyring --cleartext --output For more information, try '--help'. dpkg-source: warning: cannot verify inline signature for ./python-pdbfixer_1.9-7.dsc: no acceptable signature found dpkg-source: info: extracting python-pdbfixer in python-pdbfixer-1.9 dpkg-source: info: unpacking python-pdbfixer_1.9.orig.tar.gz dpkg-source: info: unpacking python-pdbfixer_1.9-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying a6f6430e785f6b7030d705ae1772a7c7691e7eec.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1333015/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='005fb581dea04d278e90b1021d02ce2c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1333015' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/pbuilderrc_QMjU --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/b1 --logfile b1/build.log python-pdbfixer_1.9-7.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.22+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.22-1~bpo12+1 (2025-04-25) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1333015/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 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-sequence-python3, help2man, python3, python3-legacy-cgi, python3-openmm, python3-pytest, python3-setuptools, rename dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19850 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-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-legacy-cgi; however: Package python3-legacy-cgi is not installed. pbuilder-satisfydepends-dummy depends on python3-openmm; however: Package python3-openmm is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on rename; however: Package rename 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} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libopenmm-dev{a} libopenmm8.1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-legacy-cgi{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-openmm{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pytest{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} rename{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-pygments wget 0 packages upgraded, 71 newly installed, 0 to remove and 0 not upgraded. Need to get 36.3 MB of archives. After unpacking 206 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.3-2 [861 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.3-2 [2212 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.3-1 [27.2 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025b-3 [260 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.3-2 [1953 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.3-2 [751 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.3-1 [10.2 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.3-1 [28.2 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-8 [1187 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 42 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250414 [116 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-11 [1059 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libopenmm-dev amd64 8.1.2+dfsg-11 [346 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.7.0-1 [67.4 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 66 http://deb.debian.org/debian trixie/main amd64 python3-legacy-cgi all 2.6.3-1 [16.5 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 python3-openmm amd64 8.1.2+dfsg-11 [6554 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.5-2 [250 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 rename all 2.02-1 [21.8 kB] Fetched 36.3 MB in 10s (3509 kB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (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 ... 19850 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.3-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.3-2) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.3-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_amd64.deb ... Unpacking python3.13 (3.13.3-2) ... Selecting previously unselected package libpython3-stdlib:amd64. 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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 libunistring5:amd64 (1.3-2) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Setting up autopoint (0.23.1-2) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up autoconf (2.72-3.1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up netbase (6.5) ... Setting up libopenmm8.1 (8.1.2+dfsg-11) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.17-4) ... 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 (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up libopenmm-dev (8.1.2+dfsg-11) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-8) ... Setting up libpython3.13-stdlib:amd64 (3.13.3-2) ... Setting up libpython3-stdlib:amd64 (3.13.3-1) ... Setting up python3.13 (3.13.3-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.3-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-packaging (25.0-1) ... Setting up python3-typing-extensions (4.13.2-1) ... Setting up python3-numpy (1:2.2.4+ds-1) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-legacy-cgi (2.6.3-1) ... Setting up python3-openmm (8.1.2+dfsg-11) ... /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:426: SyntaxWarning: invalid escape sequence '\S' r"(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.7.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3-pytest (8.3.5-2) ... Setting up python3-typeguard (4.4.2-1) ... Setting up debhelper (13.24.2) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-setuptools (78.1.1-0.1) ... Processing triggers for libc-bin (2.41-8) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/python-pdbfixer-1.9/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-pdbfixer_1.9-7_source.changes dpkg-buildpackage: info: source package python-pdbfixer dpkg-buildpackage: info: source version 1.9-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from python-pdbfixer-1.9/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/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 debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' rm -rf pdbfixer.egg-info make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' for TEST in test_build_and_simulate.py test_cli.py test_mutate.py; do mv pdbfixer/tests/${TEST} pdbfixer/tests/HIDE_${TEST}; done dh_auto_build I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer copying pdbfixer/pdbfixer.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer copying pdbfixer/ui.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer copying pdbfixer/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer copying pdbfixer/uiserver.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/test_removechains.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/HIDE_test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/HIDE_test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/HIDE_test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/soft.xml -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data copying pdbfixer/tests/data/4JSV.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data copying pdbfixer/tests/data/test.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/GLU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/LYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/TYR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/VAL.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/PRO.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/THR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DC.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/A.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/G.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/TRP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ALA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/NME.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DT.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ILE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/U.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ARG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/PHE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ACE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/MET.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/C.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ASP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/GLN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ASN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/SER.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/GLY.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/CYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/HIS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/LEU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/start.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/removeChains.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/addHeavyAtoms.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/convertResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/quit.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/saveFile.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/header.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/addHydrogens.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/addResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/error.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images copying pdbfixer/images/logo.png -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images copying pdbfixer/images/background.jpg -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images copying pdbfixer/images/logo.svg -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images copying pdbfixer/images/logo_small.png -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images rename 's/HIDE_//' pdbfixer/tests/HIDE_* make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' dh_auto_test -- --test-pytest I: pybuild base:311: cd /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build; python3.13 -m pytest ============================= test session starts ============================== platform linux -- Python 3.13.3, pytest-8.3.5, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pdbfixer-1.9 plugins: typeguard-4.4.2 collected 2 items pdbfixer/tests/test_removechains.py .. [100%] =============================== warnings summary =============================== :488 :488: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute :488 :488: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute :488 :488: DeprecationWarning: builtin type swigvarlink has no __module__ attribute -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================== 2 passed, 3 warnings in 6.86s ========================= make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/python3-pdbfixer/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: 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 copying pdbfixer/tests/test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests running install_lib creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_removechains.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/__pycache__/test_removechains.cpython-313-pytest-8.3.5.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__pycache__ creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/data copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data/4JSV.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/data copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data/test.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/data copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/HIDE_test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/HIDE_test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/HIDE_test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/__pycache__/pdbfixer.cpython-313.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/pdbfixer.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/ui.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/GLU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/LYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/TYR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/VAL.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/PRO.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/THR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DC.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/A.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/G.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/TRP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ALA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/NME.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DT.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ILE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/U.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ARG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/PHE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ACE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/MET.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/C.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ASP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/GLN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ASN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/SER.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/GLY.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/CYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/HIS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/LEU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/start.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/removeChains.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/addHeavyAtoms.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/convertResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/quit.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/saveFile.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/header.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/addHydrogens.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/addResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/error.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/uiserver.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/soft.xml -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/logo.png -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/background.jpg -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/logo.svg -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/logo_small.png -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_removechains.py to test_removechains.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_cli.py to test_cli.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/HIDE_test_mutate.py to HIDE_test_mutate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_build_and_simulate.py to test_build_and_simulate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_mutate.py to test_mutate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/HIDE_test_cli.py to HIDE_test_cli.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/HIDE_test_build_and_simulate.py to HIDE_test_build_and_simulate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/pdbfixer.py to pdbfixer.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/ui.py to ui.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/uiserver.py to uiserver.cpython-313.pyc running install_egg_info running egg_info creating pdbfixer.egg-info writing pdbfixer.egg-info/PKG-INFO writing dependency_links to pdbfixer.egg-info/dependency_links.txt writing entry points to pdbfixer.egg-info/entry_points.txt writing requirements to pdbfixer.egg-info/requires.txt writing top-level names to pdbfixer.egg-info/top_level.txt writing manifest file 'pdbfixer.egg-info/SOURCES.txt' reading manifest file 'pdbfixer.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'pdbfixer.egg-info/SOURCES.txt' Copying pdbfixer.egg-info to /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer-1.9.0.egg-info Skipping SOURCES.txt running install_scripts Installing pdbfixer script to /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/bin dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' PYTHONPATH=. help2man debian/python3-pdbfixer/usr/bin/pdbfixer --no-info \ --name 'Fix problems in Protein Data Bank files' \ --version-string "1.9" > pdbfixer.1 dh_installman pdbfixer.1 make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:114: replacing shebang in debian/python3-pdbfixer/usr/bin/pdbfixer debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' rm debian/python3-pdbfixer/usr/lib/python3/dist-packages/pdbfixer/tests/HIDE_* make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' 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 dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pdbfixer' in '../python3-pdbfixer_1.9-7_all.deb'. dpkg-genbuildinfo --build=binary -O../python-pdbfixer_1.9-7_amd64.buildinfo dpkg-genchanges --build=binary -O../python-pdbfixer_1.9-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from python-pdbfixer-1.9/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1333015 and its subdirectories I: Current time: Wed Jul 8 09:14:54 -12 2026 I: pbuilder-time-stamp: 1783545294 Wed Jul 8 21:14:54 UTC 2026 I: Signing ./b1/python-pdbfixer_1.9-7_amd64.buildinfo as python-pdbfixer_1.9-7_amd64.buildinfo.asc Wed Jul 8 21:14:54 UTC 2026 I: Signed ./b1/python-pdbfixer_1.9-7_amd64.buildinfo as ./b1/python-pdbfixer_1.9-7_amd64.buildinfo.asc Wed Jul 8 21:14:54 UTC 2026 - build #1 for python-pdbfixer/trixie/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Wed Jul 8 21:14:54 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-Mhxzqsn6, removing. /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jun 5 14:51 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jun 5 14:44 b2 -rw-r--r-- 1 jenkins jenkins 2196 Feb 5 07:08 python-pdbfixer_1.9-7.dsc -rw------- 1 jenkins jenkins 3339 Jun 5 14:44 rbuildlog.oPV9Faa /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/b1: total 532 -rw-r--r-- 1 jenkins jenkins 70579 Jun 5 14:51 build.log -rw-r--r-- 1 jenkins jenkins 3672 Jun 5 14:51 python-pdbfixer_1.9-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2196 Jun 5 14:51 python-pdbfixer_1.9-7.dsc -rw-r--r-- 1 jenkins jenkins 5946 Jun 5 14:51 python-pdbfixer_1.9-7_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6828 Jun 5 14:51 python-pdbfixer_1.9-7_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1113 Jun 5 14:51 python-pdbfixer_1.9-7_amd64.changes -rw-r--r-- 1 jenkins jenkins 1267 Jun 5 14:51 python-pdbfixer_1.9-7_source.changes -rw-r--r-- 1 jenkins jenkins 437520 Jun 5 14:51 python3-pdbfixer_1.9-7_all.deb /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/b2: total 0 Thu Jun 5 14:51:55 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 8 09:07:34 -12 2026 I: pbuilder-time-stamp: 1783544854 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-pdbfixer_1.9-7.dsc] I: copying [./python-pdbfixer_1.9.orig.tar.gz] I: copying [./python-pdbfixer_1.9-7.debian.tar.xz] I: Extracting source error: the following required arguments were not provided: --keyring Usage: sqv --keyring --cleartext --output For more information, try '--help'. dpkg-source: warning: cannot verify inline signature for ./python-pdbfixer_1.9-7.dsc: no acceptable signature found dpkg-source: info: extracting python-pdbfixer in python-pdbfixer-1.9 dpkg-source: info: unpacking python-pdbfixer_1.9.orig.tar.gz dpkg-source: info: unpacking python-pdbfixer_1.9-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying a6f6430e785f6b7030d705ae1772a7c7691e7eec.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1333015/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='005fb581dea04d278e90b1021d02ce2c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1333015' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/pbuilderrc_QMjU --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/b1 --logfile b1/build.log python-pdbfixer_1.9-7.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.22+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.22-1~bpo12+1 (2025-04-25) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1333015/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 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-sequence-python3, help2man, python3, python3-legacy-cgi, python3-openmm, python3-pytest, python3-setuptools, rename dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19850 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-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-legacy-cgi; however: Package python3-legacy-cgi is not installed. pbuilder-satisfydepends-dummy depends on python3-openmm; however: Package python3-openmm is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on rename; however: Package rename 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} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libopenmm-dev{a} libopenmm8.1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-legacy-cgi{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-openmm{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pytest{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} rename{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-pygments wget 0 packages upgraded, 71 newly installed, 0 to remove and 0 not upgraded. Need to get 36.3 MB of archives. After unpacking 206 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.3-2 [861 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.3-2 [2212 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.3-1 [27.2 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025b-3 [260 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.3-2 [1953 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.3-2 [751 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.3-1 [10.2 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.3-1 [28.2 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-8 [1187 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 42 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250414 [116 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-11 [1059 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libopenmm-dev amd64 8.1.2+dfsg-11 [346 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.7.0-1 [67.4 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 66 http://deb.debian.org/debian trixie/main amd64 python3-legacy-cgi all 2.6.3-1 [16.5 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 python3-openmm amd64 8.1.2+dfsg-11 [6554 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.5-2 [250 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 rename all 2.02-1 [21.8 kB] Fetched 36.3 MB in 10s (3509 kB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (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 ... 19850 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.3-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.3-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.1-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.3-2_amd64.deb ... Unpacking python3.13-minimal (3.13.3-2) ... Setting up libpython3.13-minimal:amd64 (3.13.3-2) ... Setting up libexpat1:amd64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.3-2) ... Selecting previously unselected package python3-minimal. (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 ... 20199 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.3-1_amd64.deb ... Unpacking python3-minimal (3.13.3-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-3_all.deb ... Unpacking tzdata (2025b-3) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.4.8-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.8-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.2-6_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.3-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_amd64.deb ... Unpacking python3.13 (3.13.3-2) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.3-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.3-1) ... Setting up python3-minimal (3.13.3-1) ... Selecting previously unselected package python3. (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 ... 21211 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.3-1_amd64.deb ... Unpacking python3 (3.13.3-1) ... Selecting previously unselected package python3-numpy-dev:amd64. 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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 libunistring5:amd64 (1.3-2) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Setting up autopoint (0.23.1-2) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up autoconf (2.72-3.1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up netbase (6.5) ... Setting up libopenmm8.1 (8.1.2+dfsg-11) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.17-4) ... 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 (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up libopenmm-dev (8.1.2+dfsg-11) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-8) ... Setting up libpython3.13-stdlib:amd64 (3.13.3-2) ... Setting up libpython3-stdlib:amd64 (3.13.3-1) ... Setting up python3.13 (3.13.3-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.3-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. 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Setting up python3-openmm (8.1.2+dfsg-11) ... /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:426: SyntaxWarning: invalid escape sequence '\S' r"(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.7.0-1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/python-pdbfixer-1.9/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-pdbfixer_1.9-7_source.changes dpkg-buildpackage: info: source package python-pdbfixer dpkg-buildpackage: info: source version 1.9-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from python-pdbfixer-1.9/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/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 debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' rm -rf pdbfixer.egg-info make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' for TEST in test_build_and_simulate.py test_cli.py test_mutate.py; do mv pdbfixer/tests/${TEST} pdbfixer/tests/HIDE_${TEST}; done dh_auto_build I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer copying pdbfixer/pdbfixer.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer copying pdbfixer/ui.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer copying pdbfixer/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer copying pdbfixer/uiserver.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/test_removechains.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/HIDE_test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/HIDE_test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/HIDE_test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/soft.xml -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data copying pdbfixer/tests/data/4JSV.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data copying pdbfixer/tests/data/test.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/GLU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/LYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/TYR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/VAL.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/PRO.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/THR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DC.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/A.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/G.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/TRP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ALA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/NME.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DT.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ILE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/U.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ARG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/PHE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ACE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/MET.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/C.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ASP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/GLN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ASN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/SER.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/GLY.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/CYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/HIS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/LEU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/start.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/removeChains.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/addHeavyAtoms.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/convertResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/quit.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/saveFile.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/header.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/addHydrogens.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/addResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/error.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images copying pdbfixer/images/logo.png -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images copying pdbfixer/images/background.jpg -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images copying pdbfixer/images/logo.svg -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images copying pdbfixer/images/logo_small.png -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images rename 's/HIDE_//' pdbfixer/tests/HIDE_* make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' dh_auto_test -- --test-pytest I: pybuild base:311: cd /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build; python3.13 -m pytest ============================= test session starts ============================== platform linux -- Python 3.13.3, pytest-8.3.5, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pdbfixer-1.9 plugins: typeguard-4.4.2 collected 2 items pdbfixer/tests/test_removechains.py .. [100%] =============================== warnings summary =============================== :488 :488: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute :488 :488: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute :488 :488: DeprecationWarning: builtin type swigvarlink has no __module__ attribute -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================== 2 passed, 3 warnings in 6.86s ========================= make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/python3-pdbfixer/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: 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 copying pdbfixer/tests/test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests running install_lib creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_removechains.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/__pycache__/test_removechains.cpython-313-pytest-8.3.5.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__pycache__ creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/data copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data/4JSV.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/data copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data/test.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/data copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/HIDE_test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/HIDE_test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/HIDE_test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/__pycache__/pdbfixer.cpython-313.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/pdbfixer.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/ui.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/GLU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/LYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/TYR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/VAL.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/PRO.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/THR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DC.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/A.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/G.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/TRP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ALA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/NME.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DT.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ILE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/U.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ARG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/PHE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ACE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/MET.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/C.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ASP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/GLN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ASN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/SER.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/GLY.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/CYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/HIS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/LEU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/start.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/removeChains.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/addHeavyAtoms.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/convertResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/quit.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/saveFile.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/header.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/addHydrogens.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/addResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/error.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/uiserver.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/soft.xml -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/logo.png -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/background.jpg -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/logo.svg -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/logo_small.png -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_removechains.py to test_removechains.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_cli.py to test_cli.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/HIDE_test_mutate.py to HIDE_test_mutate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_build_and_simulate.py to test_build_and_simulate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_mutate.py to test_mutate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/HIDE_test_cli.py to HIDE_test_cli.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/HIDE_test_build_and_simulate.py to HIDE_test_build_and_simulate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/pdbfixer.py to pdbfixer.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/ui.py to ui.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/uiserver.py to uiserver.cpython-313.pyc running install_egg_info running egg_info creating pdbfixer.egg-info writing pdbfixer.egg-info/PKG-INFO writing dependency_links to pdbfixer.egg-info/dependency_links.txt writing entry points to pdbfixer.egg-info/entry_points.txt writing requirements to pdbfixer.egg-info/requires.txt writing top-level names to pdbfixer.egg-info/top_level.txt writing manifest file 'pdbfixer.egg-info/SOURCES.txt' reading manifest file 'pdbfixer.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'pdbfixer.egg-info/SOURCES.txt' Copying pdbfixer.egg-info to /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer-1.9.0.egg-info Skipping SOURCES.txt running install_scripts Installing pdbfixer script to /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/bin dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' PYTHONPATH=. help2man debian/python3-pdbfixer/usr/bin/pdbfixer --no-info \ --name 'Fix problems in Protein Data Bank files' \ --version-string "1.9" > pdbfixer.1 dh_installman pdbfixer.1 make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:114: replacing shebang in debian/python3-pdbfixer/usr/bin/pdbfixer debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' rm debian/python3-pdbfixer/usr/lib/python3/dist-packages/pdbfixer/tests/HIDE_* make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' 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 dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pdbfixer' in '../python3-pdbfixer_1.9-7_all.deb'. dpkg-genbuildinfo --build=binary -O../python-pdbfixer_1.9-7_amd64.buildinfo dpkg-genchanges --build=binary -O../python-pdbfixer_1.9-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from python-pdbfixer-1.9/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1333015 and its subdirectories I: Current time: Wed Jul 8 09:14:54 -12 2026 I: pbuilder-time-stamp: 1783545294 Thu Jun 5 14:51:56 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Thu Jun 5 14:51:56 UTC 2025 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Thu Jun 5 14:51:56 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Thu Jun 5 14:51:56 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-3a5Rp7' ==================================================================================== Thu Jun 5 14:51:56 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "2 python-pdbfixer trixie /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS 1.9-7" as arguments. Thu Jun 5 14:51:56 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-0HUpWoNn" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Jun 5 14:51:56 UTC 2025 I: Downloading source for trixie/python-pdbfixer=1.9-7 Reading package lists... NOTICE: 'python-pdbfixer' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/python-team/packages/python-pdbfixer.git Please use: git clone https://salsa.debian.org/python-team/packages/python-pdbfixer.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 654 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main python-pdbfixer 1.9-7 (dsc) [2196 B] Get:2 http://deb.debian.org/debian trixie/main python-pdbfixer 1.9-7 (tar) [648 kB] Get:3 http://deb.debian.org/debian trixie/main python-pdbfixer 1.9-7 (diff) [3672 B] Fetched 654 kB in 0s (18.7 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'python-pdbfixer' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/python-team/packages/python-pdbfixer.git Please use: git clone https://salsa.debian.org/python-team/packages/python-pdbfixer.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 654 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main python-pdbfixer 1.9-7 (dsc) [2196 B] Get:2 http://deb.debian.org/debian trixie/main python-pdbfixer 1.9-7 (tar) [648 kB] Get:3 http://deb.debian.org/debian trixie/main python-pdbfixer 1.9-7 (diff) [3672 B] Fetched 654 kB in 0s (18.7 MB/s) Download complete and in download only mode ============================================================================= Re-Building python-pdbfixer in trixie on amd64 on ionos1-amd64 now. Date: Thu Jun 5 14:51:57 UTC 2025 Date UTC: Thu Jun 5 14:51:57 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/pbuilderrc_7q76 + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' python-pdbfixer = debian-installer -o python-pdbfixer = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' python-pdbfixer = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo 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.YpETjZRS/pbuilderrc_7q76 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/b2 --logfile b2/build.log python-pdbfixer_1.9-7.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Jun 6 04:51:57 +14 2025 I: pbuilder-time-stamp: 1749135117 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-pdbfixer_1.9-7.dsc] I: copying [./python-pdbfixer_1.9.orig.tar.gz] I: copying [./python-pdbfixer_1.9-7.debian.tar.xz] I: Extracting source error: the following required arguments were not provided: --keyring Usage: sqv --keyring --cleartext --output For more information, try '--help'. dpkg-source: warning: cannot verify inline signature for ./python-pdbfixer_1.9-7.dsc: no acceptable signature found dpkg-source: info: extracting python-pdbfixer in python-pdbfixer-1.9 dpkg-source: info: unpacking python-pdbfixer_1.9.orig.tar.gz dpkg-source: info: unpacking python-pdbfixer_1.9-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying a6f6430e785f6b7030d705ae1772a7c7691e7eec.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1066533/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-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 Jun 5 14:52 /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/1066533/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1066533/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=40 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=a65254af842b44e6979de35e90c34aec 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=1066533 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.YpETjZRS/pbuilderrc_7q76 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/b2 --logfile b2/build.log python-pdbfixer_1.9-7.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1066533/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 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-sequence-python3, help2man, python3, python3-legacy-cgi, python3-openmm, python3-pytest, python3-setuptools, rename dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19850 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-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-legacy-cgi; however: Package python3-legacy-cgi is not installed. pbuilder-satisfydepends-dummy depends on python3-openmm; however: Package python3-openmm is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on rename; however: Package rename 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} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libopenmm-dev{a} libopenmm8.1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-legacy-cgi{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-openmm{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pytest{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} rename{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-pygments wget 0 packages upgraded, 71 newly installed, 0 to remove and 0 not upgraded. Need to get 36.3 MB of archives. After unpacking 206 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.3-2 [861 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.3-2 [2212 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.3-1 [27.2 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025b-3 [260 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.3-2 [1953 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.3-2 [751 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.3-1 [10.2 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.3-1 [28.2 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-8 [1187 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-4 [862 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 42 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.2 [919 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250414 [116 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-11 [1059 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libopenmm-dev amd64 8.1.2+dfsg-11 [346 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.7.0-1 [67.4 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 66 http://deb.debian.org/debian trixie/main amd64 python3-legacy-cgi all 2.6.3-1 [16.5 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 python3-openmm amd64 8.1.2+dfsg-11 [6554 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.5-2 [250 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 rename all 2.02-1 [21.8 kB] Fetched 36.3 MB in 0s (91.6 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (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 ... 19850 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.3-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.3-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.1-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.3-2_amd64.deb ... Unpacking python3.13-minimal (3.13.3-2) ... Setting up libpython3.13-minimal:amd64 (3.13.3-2) ... Setting up libexpat1:amd64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.3-2) ... Selecting previously unselected package python3-minimal. (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 ... 20199 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.3-1_amd64.deb ... Unpacking python3-minimal (3.13.3-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.3-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_amd64.deb ... Unpacking python3.13 (3.13.3-2) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.3-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.3-1) ... Setting up python3-minimal (3.13.3-1) ... Selecting previously unselected package python3. (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 ... 21211 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.3-1_amd64.deb ... Unpacking python3 (3.13.3-1) ... Selecting previously unselected package python3-numpy-dev:amd64. Preparing to unpack .../01-python3-numpy-dev_1%3a2.2.4+ds-1_amd64.deb ... Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../02-libblas3_3.12.1-2_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-2) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../03-libgfortran5_14.2.0-19_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-19) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../04-liblapack3_3.12.1-2_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-2) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../05-python3-numpy_1%3a2.2.4+ds-1_amd64.deb ... Unpacking python3-numpy (1:2.2.4+ds-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. 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Selecting previously unselected package rename. Preparing to unpack .../56-rename_2.02-1_all.deb ... Unpacking rename (2.02-1) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up rename (2.02-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up tzdata (2025b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Jun 5 14:54:00 UTC 2025. Universal Time is now: Thu Jun 5 14:54:00 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... 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 libunistring5:amd64 (1.3-2) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Setting up autopoint (0.23.1-2) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up autoconf (2.72-3.1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up netbase (6.5) ... Setting up libopenmm8.1 (8.1.2+dfsg-11) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.17-4) ... 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 (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up libopenmm-dev (8.1.2+dfsg-11) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-8) ... Setting up libpython3.13-stdlib:amd64 (3.13.3-2) ... Setting up libpython3-stdlib:amd64 (3.13.3-1) ... Setting up python3.13 (3.13.3-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.3-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-packaging (25.0-1) ... Setting up python3-typing-extensions (4.13.2-1) ... Setting up python3-numpy (1:2.2.4+ds-1) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-legacy-cgi (2.6.3-1) ... Setting up python3-openmm (8.1.2+dfsg-11) ... /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:426: SyntaxWarning: invalid escape sequence '\S' r"(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.7.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3-pytest (8.3.5-2) ... Setting up python3-typeguard (4.4.2-1) ... Setting up debhelper (13.24.2) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-setuptools (78.1.1-0.1) ... Processing triggers for libc-bin (2.41-8) ... 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/1066533/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/1066533/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/python-pdbfixer-1.9/ && 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 > ../python-pdbfixer_1.9-7_source.changes dpkg-buildpackage: info: source package python-pdbfixer dpkg-buildpackage: info: source version 1.9-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from python-pdbfixer-1.9/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --buildsystem pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/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 debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' rm -rf pdbfixer.egg-info make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' for TEST in test_build_and_simulate.py test_cli.py test_mutate.py; do mv pdbfixer/tests/${TEST} pdbfixer/tests/HIDE_${TEST}; done dh_auto_build I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer copying pdbfixer/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer copying pdbfixer/uiserver.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer copying pdbfixer/pdbfixer.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer copying pdbfixer/ui.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/HIDE_test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/test_removechains.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/HIDE_test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/HIDE_test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/soft.xml -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images copying pdbfixer/images/logo_small.png -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images copying pdbfixer/images/background.jpg -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images copying pdbfixer/images/logo.png -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images copying pdbfixer/images/logo.svg -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/convertResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/addResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/header.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/error.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/addHeavyAtoms.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/saveFile.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/quit.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/addHydrogens.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/start.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html copying pdbfixer/html/removeChains.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data copying pdbfixer/tests/data/4JSV.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data copying pdbfixer/tests/data/test.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/PHE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/CYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/PRO.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DC.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/G.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/GLN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/U.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/NME.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ARG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/TRP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/THR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/GLY.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ILE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/LEU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ASN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/GLU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/A.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ALA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/LYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/SER.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DT.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ASP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/TYR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/MET.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/C.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ACE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/HIS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/VAL.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates rename 's/HIDE_//' pdbfixer/tests/HIDE_* make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' dh_auto_test -- --test-pytest I: pybuild base:311: cd /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build; python3.13 -m pytest ============================= test session starts ============================== platform linux -- Python 3.13.3, pytest-8.3.5, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pdbfixer-1.9 plugins: typeguard-4.4.2 collected 2 items pdbfixer/tests/test_removechains.py .. [100%] =============================== warnings summary =============================== :488 :488: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute :488 :488: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute :488 :488: DeprecationWarning: builtin type swigvarlink has no __module__ attribute -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================== 2 passed, 3 warnings in 8.96s ========================= make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/python3-pdbfixer/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: 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 copying pdbfixer/tests/test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests running install_lib creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/__pycache__/pdbfixer.cpython-313.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__pycache__ creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/logo_small.png -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/background.jpg -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/logo.png -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/logo.svg -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/soft.xml -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/uiserver.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/convertResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/addResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/header.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/error.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/addHeavyAtoms.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/saveFile.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/quit.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/addHydrogens.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/start.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/removeChains.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/__pycache__/test_removechains.cpython-313-pytest-8.3.5.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/HIDE_test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_removechains.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/HIDE_test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/data copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data/4JSV.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/data copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data/test.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/data copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/HIDE_test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/pdbfixer.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/PHE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/CYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/PRO.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DC.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/G.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/GLN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/U.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/NME.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ARG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/TRP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/THR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/GLY.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ILE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/LEU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ASN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/GLU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/A.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ALA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/LYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/SER.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DT.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ASP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/TYR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/MET.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/C.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ACE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/HIS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/VAL.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/ui.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/uiserver.py to uiserver.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/HIDE_test_build_and_simulate.py to HIDE_test_build_and_simulate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_removechains.py to test_removechains.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_cli.py to test_cli.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_build_and_simulate.py to test_build_and_simulate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/HIDE_test_cli.py to HIDE_test_cli.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/HIDE_test_mutate.py to HIDE_test_mutate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_mutate.py to test_mutate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/pdbfixer.py to pdbfixer.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/ui.py to ui.cpython-313.pyc running install_egg_info running egg_info creating pdbfixer.egg-info writing pdbfixer.egg-info/PKG-INFO writing dependency_links to pdbfixer.egg-info/dependency_links.txt writing entry points to pdbfixer.egg-info/entry_points.txt writing requirements to pdbfixer.egg-info/requires.txt writing top-level names to pdbfixer.egg-info/top_level.txt writing manifest file 'pdbfixer.egg-info/SOURCES.txt' reading manifest file 'pdbfixer.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'pdbfixer.egg-info/SOURCES.txt' Copying pdbfixer.egg-info to /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer-1.9.0.egg-info Skipping SOURCES.txt running install_scripts Installing pdbfixer script to /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/bin dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' PYTHONPATH=. help2man debian/python3-pdbfixer/usr/bin/pdbfixer --no-info \ --name 'Fix problems in Protein Data Bank files' \ --version-string "1.9" > pdbfixer.1 dh_installman pdbfixer.1 make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:114: replacing shebang in debian/python3-pdbfixer/usr/bin/pdbfixer debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' rm debian/python3-pdbfixer/usr/lib/python3/dist-packages/pdbfixer/tests/HIDE_* make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' 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 dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pdbfixer' in '../python3-pdbfixer_1.9-7_all.deb'. dpkg-genbuildinfo --build=binary -O../python-pdbfixer_1.9-7_amd64.buildinfo dpkg-genchanges --build=binary -O../python-pdbfixer_1.9-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from python-pdbfixer-1.9/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/1066533/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1066533/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/1066533 and its subdirectories I: Current time: Fri Jun 6 04:54:56 +14 2025 I: pbuilder-time-stamp: 1749135296 + false + set +x Thu Jun 5 14:54:56 UTC 2025 I: Signing ./b2/python-pdbfixer_1.9-7_amd64.buildinfo as python-pdbfixer_1.9-7_amd64.buildinfo.asc Thu Jun 5 14:54:57 UTC 2025 I: Signed ./b2/python-pdbfixer_1.9-7_amd64.buildinfo as ./b2/python-pdbfixer_1.9-7_amd64.buildinfo.asc Thu Jun 5 14:54:57 UTC 2025 - build #2 for python-pdbfixer/trixie/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Thu Jun 5 14:54:57 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-0HUpWoNn, removing. /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS: total 92 drwxr-xr-x 2 jenkins jenkins 4096 Jun 5 14:51 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jun 5 14:54 b2 -rw-r--r-- 1 jenkins jenkins 2196 Feb 5 07:08 python-pdbfixer_1.9-7.dsc -rw------- 1 jenkins jenkins 74205 Jun 5 14:51 rbuildlog.oPV9Faa /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/b1: total 540 -rw-r--r-- 1 jenkins jenkins 70579 Jun 5 14:51 build.log -rw-r--r-- 1 jenkins jenkins 3672 Jun 5 14:51 python-pdbfixer_1.9-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2196 Jun 5 14:51 python-pdbfixer_1.9-7.dsc -rw-r--r-- 1 jenkins jenkins 5946 Jun 5 14:51 python-pdbfixer_1.9-7_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6828 Jun 5 14:51 python-pdbfixer_1.9-7_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1113 Jun 5 14:51 python-pdbfixer_1.9-7_amd64.changes -rw-r--r-- 1 jenkins jenkins 1267 Jun 5 14:51 python-pdbfixer_1.9-7_source.changes -rw-r--r-- 1 jenkins jenkins 437520 Jun 5 14:51 python3-pdbfixer_1.9-7_all.deb /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/b2: total 532 -rw-r--r-- 1 jenkins jenkins 72494 Jun 5 14:54 build.log -rw-r--r-- 1 jenkins jenkins 3672 Jun 5 14:54 python-pdbfixer_1.9-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2196 Jun 5 14:54 python-pdbfixer_1.9-7.dsc -rw-r--r-- 1 jenkins jenkins 5935 Jun 5 14:54 python-pdbfixer_1.9-7_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6817 Jun 5 14:54 python-pdbfixer_1.9-7_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1113 Jun 5 14:54 python-pdbfixer_1.9-7_amd64.changes -rw-r--r-- 1 jenkins jenkins 1267 Jun 5 14:54 python-pdbfixer_1.9-7_source.changes -rw-r--r-- 1 jenkins jenkins 437520 Jun 5 14:54 python3-pdbfixer_1.9-7_all.deb Thu Jun 5 14:54:59 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Thu Jun 5 14:54:59 UTC 2025 I: python-pdbfixer_1.9-7_amd64.changes: Format: 1.8 Date: Wed, 05 Feb 2025 07:51:17 +0100 Source: python-pdbfixer Binary: python3-pdbfixer Architecture: all Version: 1.9-7 Distribution: unstable Urgency: medium Maintainer: Debian Python Team Changed-By: Alexandre Detiste Description: python3-pdbfixer - Fix problems in Protein Data Bank files (Python 3) Changes: python-pdbfixer (1.9-7) unstable; urgency=medium . * Team upload. * Use upstream commit to remove dep on python3-pkg-resources. Checksums-Sha1: bc12ef42d73d1b675652cf4d3828e66afd18cd2e 5946 python-pdbfixer_1.9-7_amd64.buildinfo f6559ea58286c9ad32fec9c34a73d04edca8e08c 437520 python3-pdbfixer_1.9-7_all.deb Checksums-Sha256: 6be989a31d65ea2ca98b5c5ae544a7ca80f73487794c2e8381cdcf021ffab3a2 5946 python-pdbfixer_1.9-7_amd64.buildinfo 681b7dc45a6eb9f9e9a0f5da21823bf284160e6ac2c6ec713b9bc2152c92c1a7 437520 python3-pdbfixer_1.9-7_all.deb Files: 428c116f0ecda40e244b58b29afab699 5946 python optional python-pdbfixer_1.9-7_amd64.buildinfo d680af46eb839162d74d8a2e62390dcc 437520 python optional python3-pdbfixer_1.9-7_all.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/python-pdbfixer_1.9-7.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/python-pdbfixer_1.9-7.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/python-pdbfixer_1.9-7.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/python-pdbfixer_1.9-7.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/python-pdbfixer_1.9-7_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/python-pdbfixer_1.9-7.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-06-05 14:51:55.435112236 +0000 +++ b2/build.log 2025-06-05 14:54:59.468311643 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jul 8 09:07:34 -12 2026 -I: pbuilder-time-stamp: 1783544854 +I: Current time: Fri Jun 6 04:51:57 +14 2025 +I: pbuilder-time-stamp: 1749135117 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying a6f6430e785f6b7030d705ae1772a7c7691e7eec.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1333015/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1066533/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 Jun 5 14:52 /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/1066533/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1066533/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + 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=40 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='005fb581dea04d278e90b1021d02ce2c' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1333015' - PS1='# ' - PS2='> ' + INVOCATION_ID=a65254af842b44e6979de35e90c34aec + 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=1066533 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/pbuilderrc_QMjU --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/b1 --logfile b1/build.log python-pdbfixer_1.9-7.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.YpETjZRS/pbuilderrc_7q76 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/b2 --logfile b2/build.log python-pdbfixer_1.9-7.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.22+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.22-1~bpo12+1 (2025-04-25) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1333015/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1066533/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -198,7 +230,7 @@ Get: 69 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.5-2 [250 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 rename all 2.02-1 [21.8 kB] -Fetched 36.3 MB in 10s (3509 kB/s) +Fetched 36.3 MB in 0s (91.6 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (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 ... 19850 files and directories currently installed.) @@ -440,8 +472,8 @@ Setting up tzdata (2025b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Jul 8 21:14:09 UTC 2026. -Universal Time is now: Wed Jul 8 21:14:09 UTC 2026. +Local time is now: Thu Jun 5 14:54:00 UTC 2025. +Universal Time is now: Thu Jun 5 14:54:00 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -522,7 +554,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/python-pdbfixer-1.9/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-pdbfixer_1.9-7_source.changes +I: user script /srv/workspace/pbuilder/1066533/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1066533/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/python-pdbfixer-1.9/ && 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 > ../python-pdbfixer_1.9-7_source.changes dpkg-buildpackage: info: source package python-pdbfixer dpkg-buildpackage: info: source version 1.9-7 dpkg-buildpackage: info: source distribution unstable @@ -598,67 +634,67 @@ running build running build_py creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer -copying pdbfixer/pdbfixer.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer -copying pdbfixer/ui.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer copying pdbfixer/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer copying pdbfixer/uiserver.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer +copying pdbfixer/pdbfixer.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer +copying pdbfixer/ui.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests +copying pdbfixer/tests/HIDE_test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/test_removechains.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests -copying pdbfixer/tests/HIDE_test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/HIDE_test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests -copying pdbfixer/tests/HIDE_test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests +copying pdbfixer/tests/HIDE_test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests copying pdbfixer/soft.xml -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer +creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images +copying pdbfixer/images/logo_small.png -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images +copying pdbfixer/images/background.jpg -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images +copying pdbfixer/images/logo.png -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images +copying pdbfixer/images/logo.svg -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images +creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html +copying pdbfixer/html/convertResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html +copying pdbfixer/html/addResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html +copying pdbfixer/html/header.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html +copying pdbfixer/html/error.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html +copying pdbfixer/html/addHeavyAtoms.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html +copying pdbfixer/html/saveFile.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html +copying pdbfixer/html/quit.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html +copying pdbfixer/html/addHydrogens.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html +copying pdbfixer/html/start.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html +copying pdbfixer/html/removeChains.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data copying pdbfixer/tests/data/4JSV.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data copying pdbfixer/tests/data/test.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/GLU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/LYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/TYR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/VAL.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/PHE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/CYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/PRO.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/THR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DC.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/A.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/G.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/TRP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/ALA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/NME.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/DT.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/ILE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/GLN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/U.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/NME.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ARG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/DG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/PHE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/ACE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/MET.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/C.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/ASP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/GLN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/TRP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/THR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/GLY.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/ILE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/LEU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ASN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/GLU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/A.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/ALA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/LYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/SER.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/GLY.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/CYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/DT.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/ASP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/TYR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/MET.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/C.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/ACE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates +copying pdbfixer/templates/DG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/HIS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -copying pdbfixer/templates/LEU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates -creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html -copying pdbfixer/html/start.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html -copying pdbfixer/html/removeChains.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html -copying pdbfixer/html/addHeavyAtoms.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html -copying pdbfixer/html/convertResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html -copying pdbfixer/html/quit.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html -copying pdbfixer/html/saveFile.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html -copying pdbfixer/html/header.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html -copying pdbfixer/html/addHydrogens.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html -copying pdbfixer/html/addResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html -copying pdbfixer/html/error.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html -creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images -copying pdbfixer/images/logo.png -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images -copying pdbfixer/images/background.jpg -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images -copying pdbfixer/images/logo.svg -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images -copying pdbfixer/images/logo_small.png -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images +copying pdbfixer/templates/VAL.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates rename 's/HIDE_//' pdbfixer/tests/HIDE_* make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' debian/rules override_dh_auto_test @@ -684,7 +720,7 @@ :488: DeprecationWarning: builtin type swigvarlink has no __module__ attribute -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -======================== 2 passed, 3 warnings in 6.86s ========================= +======================== 2 passed, 3 warnings in 8.96s ========================= make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild @@ -726,88 +762,88 @@ running install_lib creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer +creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__pycache__ +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/__pycache__/pdbfixer.cpython-313.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__pycache__ +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__pycache__ +creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/logo_small.png -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/background.jpg -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/logo.png -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/logo.svg -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/soft.xml -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/uiserver.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer +creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/convertResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/addResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/header.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/error.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/addHeavyAtoms.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/saveFile.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/quit.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/addHydrogens.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/start.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/removeChains.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_removechains.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__pycache__ -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/__pycache__/test_removechains.cpython-313-pytest-8.3.5.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__pycache__ +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__pycache__ +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/HIDE_test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_removechains.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/HIDE_test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/data copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data/4JSV.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/data copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/data/test.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/data copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/HIDE_test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/HIDE_test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests/HIDE_test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests -creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__pycache__ -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__pycache__ -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/__pycache__/pdbfixer.cpython-313.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/pdbfixer.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/ui.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/GLU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/LYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/TYR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/VAL.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/PHE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/CYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/PRO.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/THR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DC.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/A.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/G.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/TRP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ALA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/NME.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DT.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ILE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/GLN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/U.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/NME.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ARG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/PHE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ACE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/MET.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/C.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ASP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/GLN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/TRP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/THR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/GLY.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ILE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/LEU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ASN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/GLU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/A.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ALA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/LYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/SER.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/GLY.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/CYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DT.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ASP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/TYR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/MET.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/C.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/ACE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/DG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/HIS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/LEU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates -creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/start.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/removeChains.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/addHeavyAtoms.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/convertResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/quit.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/saveFile.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/header.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/addHydrogens.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/addResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/html/error.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/html -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/uiserver.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/soft.xml -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer -creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/logo.png -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/background.jpg -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/logo.svg -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images -copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/images/logo_small.png -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/templates/VAL.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/templates +copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/ui.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer +byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__init__.py to __init__.cpython-313.pyc +byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/uiserver.py to uiserver.cpython-313.pyc +byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/HIDE_test_build_and_simulate.py to HIDE_test_build_and_simulate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_removechains.py to test_removechains.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_cli.py to test_cli.cpython-313.pyc -byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/HIDE_test_mutate.py to HIDE_test_mutate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_build_and_simulate.py to test_build_and_simulate.cpython-313.pyc -byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_mutate.py to test_mutate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/HIDE_test_cli.py to HIDE_test_cli.cpython-313.pyc -byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/HIDE_test_build_and_simulate.py to HIDE_test_build_and_simulate.cpython-313.pyc +byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/HIDE_test_mutate.py to HIDE_test_mutate.cpython-313.pyc +byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/tests/test_mutate.py to test_mutate.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/pdbfixer.py to pdbfixer.cpython-313.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/ui.py to ui.cpython-313.pyc -byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/__init__.py to __init__.cpython-313.pyc -byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/uiserver.py to uiserver.cpython-313.pyc running install_egg_info running egg_info creating pdbfixer.egg-info @@ -859,12 +895,14 @@ 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/1066533/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1066533/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/1333015 and its subdirectories -I: Current time: Wed Jul 8 09:14:54 -12 2026 -I: pbuilder-time-stamp: 1783545294 +I: removing directory /srv/workspace/pbuilder/1066533 and its subdirectories +I: Current time: Fri Jun 6 04:54:56 +14 2025 +I: pbuilder-time-stamp: 1749135296 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/python-pdbfixer_1.9-7.diff: 90.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/python-pdbfixer_1.9-7.diff.gz b2/build.log: 85.5% -- replaced with stdout Compressing the 1st log... b1/build.log: 86.1% -- replaced with stdout Thu Jun 5 14:55:00 UTC 2025 I: diffoscope 297 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_python-pdbfixer_trixie_amd64_1749135300 + touch /var/log/reproducible-builds/diffoscope_stamp_python-pdbfixer_trixie_amd64_1749135300 + RESULT=0 + systemd-run '--description=diffoscope on python-pdbfixer/1.9-7 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_4-55598 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS --run-session -c jenkins-reproducible-trixie-diffoscope-dde1f890-a384-4190-9532-a63fb99d4326 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/dbd-tmp-t5pyvUN ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/python-pdbfixer_1.9-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/python-pdbfixer_1.9-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/python-pdbfixer_1.9-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/b1/python-pdbfixer_1.9-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/b2/python-pdbfixer_1.9-7_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_4-55598.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/python-pdbfixer_1.9-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/python-pdbfixer_1.9-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/python-pdbfixer_1.9-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/b1/python-pdbfixer_1.9-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.YpETjZRS/b2/python-pdbfixer_1.9-7_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 161ms CPU time consumed: 162ms _ _ _ _ __ _ _ __ _ _| |_| |__ ___ _ __ _ __ __| | |__ / _(_)_ _____ _ __ | '_ \| | | | __| '_ \ / _ \| '_ \ _____| '_ \ / _` | '_ \| |_| \ \/ / _ \ '__| | |_) | |_| | |_| | | | (_) | | | |_____| |_) | (_| | |_) | _| |> < __/ | | .__/ \__, |\__|_| |_|\___/|_| |_| | .__/ \__,_|_.__/|_| |_/_/\_\___|_| |_| |___/ |_| Thu Jun 5 14:55:00 UTC 2025 I: diffoscope 297 found no differences in the changes files, and a .buildinfo file also exists. Thu Jun 5 14:55:00 UTC 2025 I: python-pdbfixer from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-06-05 14:55:01] INFO: Starting at 2025-06-05 14:55:01.376583 [2025-06-05 14:55:01] INFO: Generating the pages of 1 package(s) [2025-06-05 14:55:01] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/python-pdbfixer didn't produce a buildlog, even though it has been built. [2025-06-05 14:55:01] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/python-pdbfixer_1.8.1-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/python-pdbfixer_1.8.1-2.diff.gz is missing [2025-06-05 14:55:01] INFO: Finished at 2025-06-05 14:55:01.576465, took: 0:00:00.199885 Thu Jun 5 14:55:01 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/python-pdbfixer.html Thu Jun 5 14:55:01 UTC 2025 I: Removing signed python-pdbfixer_1.9-7_amd64.buildinfo.asc files: removed './b1/python-pdbfixer_1.9-7_amd64.buildinfo.asc' removed './b2/python-pdbfixer_1.9-7_amd64.buildinfo.asc' 1749135301 amd64 trixie python-pdbfixer Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/python-pdbfixer_1.9-7.rbuild.log: 83.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/python-pdbfixer_1.9-7.rbuild.log.gz [2025-06-05 14:55:01] INFO: Starting at 2025-06-05 14:55:01.833396 [2025-06-05 14:55:01] INFO: Generating the pages of 1 package(s) [2025-06-05 14:55:02] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/python-pdbfixer_1.8.1-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/python-pdbfixer_1.8.1-2.diff.gz is missing [2025-06-05 14:55:02] INFO: Finished at 2025-06-05 14:55:02.020607, took: 0:00:00.187213 All cleanup done. Thu Jun 5 14:55:02 UTC 2025 - total duration: 0h 10m 48s. Thu Jun 5 14:55:02 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-M1nxOWEM, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 10min 49.444s CPU time consumed: 4.454s