Running as unit: rb-build-arm64_1-56850.service ==================================================================================== Tue Jan 21 14:41:22 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_1) on jenkins, called using "codethink01-arm64 codethink02-arm64" as arguments. Tue Jan 21 14:41:22 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-9q77hNMz" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Jan 21 14:41:22 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Tue Jan 21 14:41:22 UTC 2025 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-D7nuac' Tue Jan 21 14:41:23 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Tue Jan 21 14:41:23 UTC 2025 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-KM6eeQ' 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 unstable on arm64 on jenkins now. 1st build will be done on codethink01-arm64.debian.net. 2nd build will be done on codethink02-arm64.debian.net. ============================================================================= Tue Jan 21 14:41:41 UTC 2025 I: starting to build python-pdbfixer/unstable/arm64 on jenkins on '2025-01-21 14:41' Tue Jan 21 14:41:41 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_1/56850/console.log 1737470501 arm64 unstable python-pdbfixer Tue Jan 21 14:41:41 UTC 2025 I: Downloading source for unstable/python-pdbfixer=1.9-5 --2025-01-21 14:41:41-- http://deb.debian.org/debian/pool/main/p/python-pdbfixer/python-pdbfixer_1.9-5.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_1.9-5.dsc’ 0K .. 100% 337M=0s 2025-01-21 14:41:41 (337 MB/s) - ‘python-pdbfixer_1.9-5.dsc’ saved [2196/2196] --2025-01-21 14:41:41-- http://deb.debian.org/debian/pool/main/p/python-pdbfixer/python-pdbfixer_1.9-5.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_1.9-5.dsc’ 0K .. 100% 337M=0s 2025-01-21 14:41:41 (337 MB/s) - ‘python-pdbfixer_1.9-5.dsc’ saved [2196/2196] Tue Jan 21 14:41:41 UTC 2025 I: python-pdbfixer_1.9-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-pdbfixer Binary: python3-pdbfixer Architecture: all Version: 1.9-5 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 4a2823d853a1a7bab1ab90fc2432a45ce4091832 3140 python-pdbfixer_1.9-5.debian.tar.xz Checksums-Sha256: 88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb 648085 python-pdbfixer_1.9.orig.tar.gz af02516814ab70d308abdb7f68227163658e27c147f15053772a975e4044f346 3140 python-pdbfixer_1.9-5.debian.tar.xz Files: 48fc0c9c12eda19e786acbc9e62433f5 648085 python-pdbfixer_1.9.orig.tar.gz e5fe73871efc0b74c7866973da1ddae0 3140 python-pdbfixer_1.9-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEEj23hBDd/OxHnQXSHMfMURUShdBoFAmeNI48RHHRjaGV0QGRl Ymlhbi5vcmcACgkQMfMURUShdBoVJxAAtdirNFmz8DdYi9FpyzS1VjkSH0fuc0+c PACc3+hvuQACiA+ZlzgwWfjlA6CK49Vco9C0C8nCo4kap70wIltqYa8RlCnw+hMr thKQCzueNVtt9I0M8awjgOZ8seGT67COQjh4/C4EBJaEXmxwRMZHoLijPPg9Hk79 3WrS47ocncGRHRvcIm0RSrpSDcD+Y0bxReqncXzifSsIvGSbZUCM+R1Qbs82yPOE oOu95BXYwm9enKosEOpespi2rwl/YA4dzztChOUup41HkGe1XOkVfGE6SjRocHD6 NHI/i/Ec6JWkl04G+BX+I8rDaQaminFPSrfFCmA3vhZkARDsBud68Kgz9xMwPVvG lXDDS0PmWgAHSgnXKHliUAnxhEvFoNaRktM8nKYZTkOMdUqL3C09zBgLbm8Ea5HP 255sJvOot0FM8U77w9H6lzyC8SYLTjqbj1fp+yF97CW4KDLWGgjtknogxu37kRsB +pxlOoZGJFN8gzfrg7jQ7xbgWYcT8EEE0Bw53NHbpb6ENSuaCaylZqvQICBHa2XN nf9nk6T5ZuSeeRTlldN+rYdiDrfxjesOXD3dHlFL6DZZDhHa7qM9fXwVfUlb+30r HCOLpMZbFr4Xl1lTKkFf/tjVMqaDX6nhs3kRQ9hSn/3MbrY0/fSRLQ8dtNXpDtv6 oY/lbdYGx4k= =m4/i -----END PGP SIGNATURE----- Tue Jan 21 14:41:41 UTC 2025 I: Checking whether the package is not for us Tue Jan 21 14:41:41 UTC 2025 I: Starting 1st build on remote node codethink01-arm64.debian.net. Tue Jan 21 14:41:41 UTC 2025 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Tue Jan 21 14:41:41 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Tue Jan 21 14:41:41 UTC 2025 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-nPw0Gj' ==================================================================================== Mon Feb 23 21:04:43 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink01-arm64, called using "1 python-pdbfixer unstable /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f 1.9-5" as arguments. Mon Feb 23 21:04:43 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-ekKHCyQg" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Feb 23 21:04:43 UTC 2026 I: Downloading source for unstable/python-pdbfixer=1.9-5 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 653 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main python-pdbfixer 1.9-5 (dsc) [2196 B] Get:2 http://deb.debian.org/debian unstable/main python-pdbfixer 1.9-5 (tar) [648 kB] Get:3 http://deb.debian.org/debian unstable/main python-pdbfixer 1.9-5 (diff) [3140 B] Fetched 653 kB in 0s (5268 kB/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 653 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main python-pdbfixer 1.9-5 (dsc) [2196 B] Get:2 http://deb.debian.org/debian unstable/main python-pdbfixer 1.9-5 (tar) [648 kB] Get:3 http://deb.debian.org/debian unstable/main python-pdbfixer 1.9-5 (diff) [3140 B] Fetched 653 kB in 0s (5268 kB/s) Download complete and in download only mode ============================================================================= Building python-pdbfixer in unstable on arm64 on codethink01-arm64 now. Date: Mon Feb 23 21:04:43 GMT 2026 Date UTC: Mon Feb 23 21:04:43 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: Mon Feb 23 09:04:43 -12 2026 I: pbuilder-time-stamp: 1771880683 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-pdbfixer_1.9-5.dsc] I: copying [./python-pdbfixer_1.9.orig.tar.gz] I: copying [./python-pdbfixer_1.9-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./python-pdbfixer_1.9-5.dsc: unsupported subcommand 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_1.9-5.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3141614/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='f5bdfd06eeb5461ea97d9e5b91583efc' 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='3141614' 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.VczGEe8f/pbuilderrc_8NZC --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/b1 --logfile b1/build.log python-pdbfixer_1.9-5.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3141614/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: arm64 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 ... 19965 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} libicu72{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-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 42.2 MB of archives. After unpacking 243 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.1-3 [852 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.1-3 [1990 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025a-1 [259 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.1-3 [1912 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.1-3 [740 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.1-2 [28.0 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-2 [539 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 37 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 52 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.6.0-1 [720 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250108 [113 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-14 [361 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libopenmm8.1 arm64 8.1.2+dfsg-2 [921 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libopenmm-dev arm64 8.1.2+dfsg-2 [330 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-legacy-cgi all 2.6.1-2 [16.1 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [3815 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-openmm arm64 8.1.2+dfsg-2 [6665 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.4-1 [250 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 rename all 2.02-1 [21.8 kB] Fetched 42.2 MB in 0s (106 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 ... 19965 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.1-3_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.1-3) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.1-3_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.1-3) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.1-3_arm64.deb ... Unpacking python3.13 (3.13.1-3) ... 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Preparing to unpack .../55-python3-pytest_8.3.4-1_all.deb ... Unpacking python3-pytest (8.3.4-1) ... Selecting previously unselected package rename. Preparing to unpack .../56-rename_2.02-1_all.deb ... Unpacking rename (2.02-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-6) ... Setting up bsdextrautils (2.40.4-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... 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 (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Feb 23 21:05:03 UTC 2026. Universal Time is now: Mon Feb 23 21:05:03 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libunistring5:arm64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up libgfortran5:arm64 (14.2.0-14) ... Setting up autoconf (2.72-3) ... Setting up libffi8:arm64 (3.4.6-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up netbase (6.4) ... Setting up libopenmm8.1 (8.1.2+dfsg-2) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-2) ... Setting up libopenmm-dev (8.1.2+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (20) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:arm64 (3.13.1-3) ... Setting up libpython3-stdlib:arm64 (3.13.1-2) ... Setting up python3.13 (3.13.1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.1-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-packaging (24.2-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-numpy (1:1.26.4+ds-13) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-legacy-cgi (2.6.1-2) ... Setting up python3-openmm (8.1.2+dfsg-2) ... /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' """ Tokenizer method for the mmCIF syntax file - /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' pattern = re.compile('bias_(.*)_(.*)\.npy') /usr/lib/python3/dist-packages/openmm/openmm.py:1556: SyntaxWarning: invalid escape sequence '\S' match = re.search("<([^?]\S*)", inputString) Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-pytest (8.3.4-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up debhelper (13.24.1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-setuptools (75.6.0-1) ... Setting up dh-python (6.20250108) ... Processing triggers for libc-bin (2.40-5) ... 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_1.9-5_source.changes dpkg-buildpackage: info: source package python-pdbfixer dpkg-buildpackage: info: source version 1.9-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 running clean removing '/build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build' (and everything under it) 'build/bdist.linux-aarch64' 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 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 running build running build_py creating /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/ui.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/__init__.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_mutate.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/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/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/test.pdb -> /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 creating /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/U.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/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/SER.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/PHE.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/MET.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/LEU.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/HIS.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/GLU.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/G.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/DG.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/DA.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/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/ASN.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/ALA.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/A.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/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/logo.svg -> /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 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/saveFile.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/quit.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/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/addHydrogens.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 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 3.13.1, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pdbfixer-1.9 plugins: typeguard-4.4.1 collected 2 items pdbfixer/tests/test_removechains.py .. [100%] =============================== warnings summary =============================== pdbfixer/pdbfixer.py:58 /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/pdbfixer.py:58: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import resource_filename -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ========================= 2 passed, 1 warning in 6.91s ========================= 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 running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying pdbfixer/tests/test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests 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 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/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/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/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/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/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/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/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/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/start.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/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/images/logo_small.png -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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_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_mutate.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__/test_removechains.cpython-313-pytest-8.3.4.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__ 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/__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/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/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/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_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/__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/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/uiserver.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/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_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_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/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/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_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/__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/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/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 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_1.9-5_all.deb'. dpkg-genbuildinfo --build=binary -O../python-pdbfixer_1.9-5_arm64.buildinfo dpkg-genchanges --build=binary -O../python-pdbfixer_1.9-5_arm64.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/3141614 and its subdirectories I: Current time: Mon Feb 23 09:05:34 -12 2026 I: pbuilder-time-stamp: 1771880734 Mon Feb 23 21:05:34 UTC 2026 I: Signing ./b1/python-pdbfixer_1.9-5_arm64.buildinfo as python-pdbfixer_1.9-5_arm64.buildinfo.asc Mon Feb 23 21:05:34 UTC 2026 I: Signed ./b1/python-pdbfixer_1.9-5_arm64.buildinfo as ./b1/python-pdbfixer_1.9-5_arm64.buildinfo.asc Mon Feb 23 21:05:34 UTC 2026 - build #1 for python-pdbfixer/unstable/arm64 on codethink01-arm64 done. Starting cleanup. All cleanup done. Mon Feb 23 21:05:34 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-ekKHCyQg, removing. /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 14:42 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 14:41 b2 -rw-r--r-- 1 jenkins jenkins 2196 Jan 19 16:16 python-pdbfixer_1.9-5.dsc -rw------- 1 jenkins jenkins 3351 Jan 21 14:41 rbuildlog.dETMhdc /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/b1: total 536 -rw-r--r-- 1 jenkins jenkins 71639 Jan 21 14:42 build.log -rw-r--r-- 1 jenkins jenkins 3140 Jan 21 14:42 python-pdbfixer_1.9-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2196 Jan 21 14:42 python-pdbfixer_1.9-5.dsc -rw-r--r-- 1 jenkins jenkins 5991 Jan 21 14:42 python-pdbfixer_1.9-5_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6873 Jan 21 14:42 python-pdbfixer_1.9-5_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1189 Jan 21 14:42 python-pdbfixer_1.9-5_arm64.changes -rw-r--r-- 1 jenkins jenkins 1343 Jan 21 14:42 python-pdbfixer_1.9-5_source.changes -rw-r--r-- 1 jenkins jenkins 438388 Jan 21 14:42 python3-pdbfixer_1.9-5_all.deb /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/b2: total 0 Tue Jan 21 14:42:35 UTC 2025 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 23 09:04:43 -12 2026 I: pbuilder-time-stamp: 1771880683 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-pdbfixer_1.9-5.dsc] I: copying [./python-pdbfixer_1.9.orig.tar.gz] I: copying [./python-pdbfixer_1.9-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./python-pdbfixer_1.9-5.dsc: unsupported subcommand 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_1.9-5.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3141614/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='f5bdfd06eeb5461ea97d9e5b91583efc' 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='3141614' 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.VczGEe8f/pbuilderrc_8NZC --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/b1 --logfile b1/build.log python-pdbfixer_1.9-5.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3141614/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: arm64 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 ... 19965 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} libicu72{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-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 42.2 MB of archives. After unpacking 243 MB will be used. Writing extended state information... 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libreadline8t64 arm64 8.2-6 [159 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.1-3 [1912 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.1-3 [740 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.1-2 [28.0 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-2 [539 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 37 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 52 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.6.0-1 [720 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250108 [113 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-14 [361 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libopenmm8.1 arm64 8.1.2+dfsg-2 [921 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libopenmm-dev arm64 8.1.2+dfsg-2 [330 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-legacy-cgi all 2.6.1-2 [16.1 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [3815 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-openmm arm64 8.1.2+dfsg-2 [6665 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.4-1 [250 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 rename all 2.02-1 [21.8 kB] Fetched 42.2 MB in 0s (106 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 ... 19965 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.1-3_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.1-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.1-3_arm64.deb ... Unpacking python3.13-minimal (3.13.1-3) ... Setting up libpython3.13-minimal:arm64 (3.13.1-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.1-3) ... 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 ... 20314 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_arm64.deb ... Unpacking python3-minimal (3.13.1-2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.1-3_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.1-3) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.1-3_arm64.deb ... Unpacking python3.13 (3.13.1-3) ... 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Preparing to unpack .../55-python3-pytest_8.3.4-1_all.deb ... Unpacking python3-pytest (8.3.4-1) ... Selecting previously unselected package rename. Preparing to unpack .../56-rename_2.02-1_all.deb ... Unpacking rename (2.02-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-6) ... Setting up bsdextrautils (2.40.4-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... 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 (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Feb 23 21:05:03 UTC 2026. Universal Time is now: Mon Feb 23 21:05:03 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libunistring5:arm64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up libgfortran5:arm64 (14.2.0-14) ... Setting up autoconf (2.72-3) ... Setting up libffi8:arm64 (3.4.6-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up netbase (6.4) ... Setting up libopenmm8.1 (8.1.2+dfsg-2) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-2) ... Setting up libopenmm-dev (8.1.2+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (20) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:arm64 (3.13.1-3) ... Setting up libpython3-stdlib:arm64 (3.13.1-2) ... Setting up python3.13 (3.13.1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.1-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-packaging (24.2-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-numpy (1:1.26.4+ds-13) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-legacy-cgi (2.6.1-2) ... Setting up python3-openmm (8.1.2+dfsg-2) ... /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' """ Tokenizer method for the mmCIF syntax file - /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' pattern = re.compile('bias_(.*)_(.*)\.npy') /usr/lib/python3/dist-packages/openmm/openmm.py:1556: SyntaxWarning: invalid escape sequence '\S' match = re.search("<([^?]\S*)", inputString) Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-pytest (8.3.4-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up debhelper (13.24.1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-setuptools (75.6.0-1) ... Setting up dh-python (6.20250108) ... Processing triggers for libc-bin (2.40-5) ... 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_1.9-5_source.changes dpkg-buildpackage: info: source package python-pdbfixer dpkg-buildpackage: info: source version 1.9-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 running clean removing '/build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build' (and everything under it) 'build/bdist.linux-aarch64' 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 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 running build running build_py creating /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/ui.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/__init__.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_mutate.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/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/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/test.pdb -> /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 creating /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/U.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/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/SER.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/PHE.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/MET.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/LEU.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/HIS.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/GLU.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/G.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/DG.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/DA.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/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/ASN.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/ALA.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/A.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/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/logo.svg -> /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 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/saveFile.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/quit.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/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/addHydrogens.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 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 3.13.1, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pdbfixer-1.9 plugins: typeguard-4.4.1 collected 2 items pdbfixer/tests/test_removechains.py .. [100%] =============================== warnings summary =============================== pdbfixer/pdbfixer.py:58 /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/pdbfixer.py:58: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import resource_filename -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ========================= 2 passed, 1 warning in 6.91s ========================= 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 running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying pdbfixer/tests/test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests 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 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/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/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/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/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/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/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/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/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/start.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/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/images/logo_small.png -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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_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_mutate.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__/test_removechains.cpython-313-pytest-8.3.4.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__ 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/__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/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/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/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_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/__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/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/uiserver.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/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_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_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/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/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_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/__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/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/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 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_1.9-5_all.deb'. dpkg-genbuildinfo --build=binary -O../python-pdbfixer_1.9-5_arm64.buildinfo dpkg-genchanges --build=binary -O../python-pdbfixer_1.9-5_arm64.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/3141614 and its subdirectories I: Current time: Mon Feb 23 09:05:34 -12 2026 I: pbuilder-time-stamp: 1771880734 Tue Jan 21 14:42:36 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink02-arm64.debian.net. Tue Jan 21 14:42:36 UTC 2025 I: Preparing to do remote build '2' on codethink02-arm64.debian.net. Tue Jan 21 14:42:36 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Tue Jan 21 14:42:36 UTC 2025 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-5RfchH' ==================================================================================== Tue Jan 21 14:42:38 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink02-arm64, called using "2 python-pdbfixer unstable /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f 1.9-5" as arguments. Tue Jan 21 14:42:38 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-2HZIkIcl" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Jan 21 14:42:38 UTC 2025 I: Downloading source for unstable/python-pdbfixer=1.9-5 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 653 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main python-pdbfixer 1.9-5 (dsc) [2196 B] Get:2 http://deb.debian.org/debian unstable/main python-pdbfixer 1.9-5 (tar) [648 kB] Get:3 http://deb.debian.org/debian unstable/main python-pdbfixer 1.9-5 (diff) [3140 B] Fetched 653 kB in 0s (21.3 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 653 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main python-pdbfixer 1.9-5 (dsc) [2196 B] Get:2 http://deb.debian.org/debian unstable/main python-pdbfixer 1.9-5 (tar) [648 kB] Get:3 http://deb.debian.org/debian unstable/main python-pdbfixer 1.9-5 (diff) [3140 B] Fetched 653 kB in 0s (21.3 MB/s) Download complete and in download only mode ============================================================================= Re-Building python-pdbfixer in unstable on arm64 on codethink02-arm64 now. Date: Tue Jan 21 14:42:38 GMT 2025 Date UTC: Tue Jan 21 14:42:38 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/pbuilderrc_7s4N + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${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.VczGEe8f/pbuilderrc_7s4N --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/b2 --logfile b2/build.log python-pdbfixer_1.9-5.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: Wed Jan 22 04:42:39 +14 2025 I: pbuilder-time-stamp: 1737470559 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-pdbfixer_1.9-5.dsc] I: copying [./python-pdbfixer_1.9.orig.tar.gz] I: copying [./python-pdbfixer_1.9-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./python-pdbfixer_1.9-5.dsc: unsupported subcommand 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_1.9-5.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3460356/tmp/hooks/D01_modify_environment starting debug: Running on codethink02-arm64. 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 Jan 21 14:42 /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/3460356/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3460356/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]="aarch64-unknown-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=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=d6a04917dafa4c2f9ed917961881d726 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=3460356 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.VczGEe8f/pbuilderrc_7s4N --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/b2 --logfile b2/build.log python-pdbfixer_1.9-5.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3460356/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: arm64 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 ... 19965 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} libicu72{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-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 42.2 MB of archives. After unpacking 243 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.1-3 [852 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.1-3 [1990 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025a-1 [259 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.1-3 [1912 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.1-3 [740 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.1-2 [28.0 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-2 [539 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 37 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 52 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.6.0-1 [720 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250108 [113 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-14 [361 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libopenmm8.1 arm64 8.1.2+dfsg-2 [921 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libopenmm-dev arm64 8.1.2+dfsg-2 [330 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-legacy-cgi all 2.6.1-2 [16.1 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [3815 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-openmm arm64 8.1.2+dfsg-2 [6665 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.4-1 [250 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 rename all 2.02-1 [21.8 kB] Fetched 42.2 MB in 1s (53.0 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 ... 19965 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.1-3_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.1-3) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.1-3_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.1-3) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.1-3_arm64.deb ... Unpacking python3.13 (3.13.1-3) ... 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Preparing to unpack .../55-python3-pytest_8.3.4-1_all.deb ... Unpacking python3-pytest (8.3.4-1) ... Selecting previously unselected package rename. Preparing to unpack .../56-rename_2.02-1_all.deb ... Unpacking rename (2.02-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-6) ... Setting up bsdextrautils (2.40.4-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... 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 (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jan 21 14:43:46 UTC 2025. Universal Time is now: Tue Jan 21 14:43:46 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libunistring5:arm64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up libgfortran5:arm64 (14.2.0-14) ... Setting up autoconf (2.72-3) ... Setting up libffi8:arm64 (3.4.6-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up netbase (6.4) ... Setting up libopenmm8.1 (8.1.2+dfsg-2) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-2) ... Setting up libopenmm-dev (8.1.2+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (20) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:arm64 (3.13.1-3) ... Setting up libpython3-stdlib:arm64 (3.13.1-2) ... Setting up python3.13 (3.13.1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.1-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-packaging (24.2-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-numpy (1:1.26.4+ds-13) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-legacy-cgi (2.6.1-2) ... Setting up python3-openmm (8.1.2+dfsg-2) ... /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' """ Tokenizer method for the mmCIF syntax file - /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' pattern = re.compile('bias_(.*)_(.*)\.npy') /usr/lib/python3/dist-packages/openmm/openmm.py:1556: SyntaxWarning: invalid escape sequence '\S' match = re.search("<([^?]\S*)", inputString) Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-pytest (8.3.4-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up debhelper (13.24.1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-setuptools (75.6.0-1) ... Setting up dh-python (6.20250108) ... Processing triggers for libc-bin (2.40-5) ... 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/3460356/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3460356/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_1.9-5_source.changes dpkg-buildpackage: info: source package python-pdbfixer dpkg-buildpackage: info: source version 1.9-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 running clean removing '/build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build' (and everything under it) 'build/bdist.linux-aarch64' 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 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 running build running build_py creating /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/ui.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/__init__.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_mutate.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/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/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/test.pdb -> /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 creating /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/U.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/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/SER.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/PHE.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/MET.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/LEU.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/HIS.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/GLU.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/G.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/DG.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/DA.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/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/ASN.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/ALA.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/A.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/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/logo.svg -> /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 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/saveFile.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/quit.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/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/addHydrogens.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 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 3.13.1, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pdbfixer-1.9 plugins: typeguard-4.4.1 collected 2 items pdbfixer/tests/test_removechains.py .. [100%] =============================== warnings summary =============================== pdbfixer/pdbfixer.py:58 /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/pdbfixer.py:58: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import resource_filename -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================== 2 passed, 1 warning in 44.68s ========================= 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 running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying pdbfixer/tests/test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.13_pdbfixer/build/pdbfixer/tests 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 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/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/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/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/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/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/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/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/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/start.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/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/images/logo_small.png -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.13/dist-packages/pdbfixer/images 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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_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_mutate.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__/test_removechains.cpython-313-pytest-8.3.4.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__ 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/__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/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/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/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_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/__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/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/uiserver.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/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_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_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/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/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_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/__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/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/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 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_1.9-5_all.deb'. dpkg-genbuildinfo --build=binary -O../python-pdbfixer_1.9-5_arm64.buildinfo dpkg-genchanges --build=binary -O../python-pdbfixer_1.9-5_arm64.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/3460356/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3460356/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/3460356 and its subdirectories I: Current time: Wed Jan 22 04:46:14 +14 2025 + false + set +x I: pbuilder-time-stamp: 1737470774 Tue Jan 21 14:46:14 UTC 2025 I: Signing ./b2/python-pdbfixer_1.9-5_arm64.buildinfo as python-pdbfixer_1.9-5_arm64.buildinfo.asc Tue Jan 21 14:46:14 UTC 2025 I: Signed ./b2/python-pdbfixer_1.9-5_arm64.buildinfo as ./b2/python-pdbfixer_1.9-5_arm64.buildinfo.asc Tue Jan 21 14:46:14 UTC 2025 - build #2 for python-pdbfixer/unstable/arm64 on codethink02-arm64 done. Starting cleanup. All cleanup done. Tue Jan 21 14:46:14 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-2HZIkIcl, removing. /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f: total 92 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 14:42 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jan 21 14:46 b2 -rw-r--r-- 1 jenkins jenkins 2196 Jan 19 16:16 python-pdbfixer_1.9-5.dsc -rw------- 1 jenkins jenkins 75291 Jan 21 14:42 rbuildlog.dETMhdc /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/b1: total 544 -rw-r--r-- 1 jenkins jenkins 71639 Jan 21 14:42 build.log -rw-r--r-- 1 jenkins jenkins 3140 Jan 21 14:42 python-pdbfixer_1.9-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2196 Jan 21 14:42 python-pdbfixer_1.9-5.dsc -rw-r--r-- 1 jenkins jenkins 5991 Jan 21 14:42 python-pdbfixer_1.9-5_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6873 Jan 21 14:42 python-pdbfixer_1.9-5_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1189 Jan 21 14:42 python-pdbfixer_1.9-5_arm64.changes -rw-r--r-- 1 jenkins jenkins 1343 Jan 21 14:42 python-pdbfixer_1.9-5_source.changes -rw-r--r-- 1 jenkins jenkins 438388 Jan 21 14:42 python3-pdbfixer_1.9-5_all.deb /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/b2: total 536 -rw-r--r-- 1 jenkins jenkins 73585 Jan 21 14:46 build.log -rw-r--r-- 1 jenkins jenkins 3140 Jan 21 14:46 python-pdbfixer_1.9-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2196 Jan 21 14:46 python-pdbfixer_1.9-5.dsc -rw-r--r-- 1 jenkins jenkins 5991 Jan 21 14:46 python-pdbfixer_1.9-5_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6873 Jan 21 14:46 python-pdbfixer_1.9-5_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1189 Jan 21 14:46 python-pdbfixer_1.9-5_arm64.changes -rw-r--r-- 1 jenkins jenkins 1343 Jan 21 14:46 python-pdbfixer_1.9-5_source.changes -rw-r--r-- 1 jenkins jenkins 438388 Jan 21 14:46 python3-pdbfixer_1.9-5_all.deb Tue Jan 21 14:46:15 UTC 2025 I: Deleting $TMPDIR on codethink02-arm64.debian.net. Tue Jan 21 14:46:16 UTC 2025 I: python-pdbfixer_1.9-5_arm64.changes: Format: 1.8 Date: Sun, 19 Jan 2025 16:30:04 +0100 Source: python-pdbfixer Binary: python3-pdbfixer Architecture: all Version: 1.9-5 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 (1.9-5) unstable; urgency=medium . * Team upload. * Add a temporary python3-setuptools dependency to untangle numpy 1:1.26.4+ds-13 transition. The real problem lies in "openmm". Checksums-Sha1: 7287fd4b6d0230b1af25928900a33b13e5307dd3 5991 python-pdbfixer_1.9-5_arm64.buildinfo d3586c8101fccd2238042a10119db59dae57243f 438388 python3-pdbfixer_1.9-5_all.deb Checksums-Sha256: a7dd4193df89b73f3eee4152f4ecfb5d675e42d84c41409635f862e41036eb32 5991 python-pdbfixer_1.9-5_arm64.buildinfo 9d287b367ab2c6d88a6f9a0ad09248c34ef4ff661e602ee928a0d8eb4d04ce2e 438388 python3-pdbfixer_1.9-5_all.deb Files: 3d5e869bcc1b98a95963da46c2e36f24 5991 python optional python-pdbfixer_1.9-5_arm64.buildinfo b0d96d09790ad0713b7030be74362723 438388 python optional python3-pdbfixer_1.9-5_all.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/python-pdbfixer_1.9-5.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/python-pdbfixer_1.9-5.rbuild.log.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-01-21 14:42:35.761857606 +0000 +++ b2/build.log 2025-01-21 14:46:15.775988492 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Feb 23 09:04:43 -12 2026 -I: pbuilder-time-stamp: 1771880683 +I: Current time: Wed Jan 22 04:42:39 +14 2025 +I: pbuilder-time-stamp: 1737470559 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -22,52 +22,84 @@ dpkg-source: info: unpacking python-pdbfixer_1.9-5.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3141614/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3460356/tmp/hooks/D01_modify_environment starting +debug: Running on codethink02-arm64. +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 Jan 21 14:42 /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/3460356/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3460356/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='f5bdfd06eeb5461ea97d9e5b91583efc' - 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='3141614' - PS1='# ' - PS2='> ' + INVOCATION_ID=d6a04917dafa4c2f9ed917961881d726 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=3460356 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.VczGEe8f/pbuilderrc_8NZC --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/b1 --logfile b1/build.log python-pdbfixer_1.9-5.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.VczGEe8f/pbuilderrc_7s4N --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/b2 --logfile b2/build.log python-pdbfixer_1.9-5.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink01-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3141614/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3460356/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -190,7 +222,7 @@ Get: 69 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.4-1 [250 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 rename all 2.02-1 [21.8 kB] -Fetched 42.2 MB in 0s (106 MB/s) +Fetched 42.2 MB in 1s (53.0 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 ... 19965 files and directories currently installed.) @@ -433,8 +465,8 @@ Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Feb 23 21:05:03 UTC 2026. -Universal Time is now: Mon Feb 23 21:05:03 UTC 2026. +Local time is now: Tue Jan 21 14:43:46 UTC 2025. +Universal Time is now: Tue Jan 21 14:43:46 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -556,7 +588,11 @@ 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_1.9-5_source.changes +I: user script /srv/workspace/pbuilder/3460356/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3460356/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_1.9-5_source.changes dpkg-buildpackage: info: source package python-pdbfixer dpkg-buildpackage: info: source version 1.9-5 dpkg-buildpackage: info: source distribution unstable @@ -674,7 +710,7 @@ from pkg_resources import resource_filename -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -========================= 2 passed, 1 warning in 6.91s ========================= +======================== 2 passed, 1 warning in 44.68s ========================= make[1]: Leaving directory '/build/reproducible-path/python-pdbfixer-1.9' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild @@ -835,12 +871,14 @@ 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/3460356/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3460356/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/3141614 and its subdirectories -I: Current time: Mon Feb 23 09:05:34 -12 2026 -I: pbuilder-time-stamp: 1771880734 +I: removing directory /srv/workspace/pbuilder/3460356 and its subdirectories +I: Current time: Wed Jan 22 04:46:14 +14 2025 +I: pbuilder-time-stamp: 1737470774 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/python-pdbfixer_1.9-5.diff: 66.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/python-pdbfixer_1.9-5.diff.gz b2/build.log: 85.3% -- replaced with stdout Compressing the 1st log... b1/build.log: 86.0% -- replaced with stdout Tue Jan 21 14:46:17 UTC 2025 I: diffoscope 285 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_python-pdbfixer_unstable_arm64_1737470777 + touch /var/log/reproducible-builds/diffoscope_stamp_python-pdbfixer_unstable_arm64_1737470777 + RESULT=0 + systemd-run '--description=diffoscope on python-pdbfixer/1.9-5 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_1-56850 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f --run-session -c jenkins-reproducible-unstable-diffoscope-55463b15-4345-4bd3-888f-caa19523789f -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/dbd-tmp-klnG33C ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/python-pdbfixer_1.9-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/python-pdbfixer_1.9-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/python-pdbfixer_1.9-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/b1/python-pdbfixer_1.9-5_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/b2/python-pdbfixer_1.9-5_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_1-56850.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/python-pdbfixer_1.9-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/python-pdbfixer_1.9-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/python-pdbfixer_1.9-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/b1/python-pdbfixer_1.9-5_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.VczGEe8f/b2/python-pdbfixer_1.9-5_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.348s) 0.348s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.018s) 0.018s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 668ms CPU time consumed: 670ms _ _ _ _ __ _ _ __ _ _| |_| |__ ___ _ __ _ __ __| | |__ / _(_)_ _____ _ __ | '_ \| | | | __| '_ \ / _ \| '_ \ _____| '_ \ / _` | '_ \| |_| \ \/ / _ \ '__| | |_) | |_| | |_| | | | (_) | | | |_____| |_) | (_| | |_) | _| |> < __/ | | .__/ \__, |\__|_| |_|\___/|_| |_| | .__/ \__,_|_.__/|_| |_/_/\_\___|_| |_| |___/ |_| Tue Jan 21 14:46:19 UTC 2025 I: diffoscope 285 found no differences in the changes files, and a .buildinfo file also exists. Tue Jan 21 14:46:19 UTC 2025 I: python-pdbfixer from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-01-21 14:46:19] INFO: Starting at 2025-01-21 14:46:19.620296 [2025-01-21 14:46:19] INFO: Generating the pages of 1 package(s) [2025-01-21 14:46:19] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/python-pdbfixer didn't produce a buildlog, even though it has been built. [2025-01-21 14:46:19] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/python-pdbfixer_1.9-5.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/python-pdbfixer_1.9-5.diff.gz is missing [2025-01-21 14:46:19] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/python-pdbfixer_1.9-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/python-pdbfixer_1.9-4.diff.gz is missing [2025-01-21 14:46:20] 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 [2025-01-21 14:46:20] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/python-pdbfixer_1.8.1-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/python-pdbfixer_1.8.1-2.diff.gz is missing [2025-01-21 14:46:20] INFO: Finished at 2025-01-21 14:46:20.023817, took: 0:00:00.403525 Tue Jan 21 14:46:20 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/python-pdbfixer.html Tue Jan 21 14:46:20 UTC 2025 I: Submitting .buildinfo files to external archives: Tue Jan 21 14:46:20 UTC 2025 I: Submitting 8.0K b1/python-pdbfixer_1.9-5_arm64.buildinfo.asc https://buildinfo.debian.net/7287fd4b6d0230b1af25928900a33b13e5307dd3/python-pdbfixer_1.9-5_all Tue Jan 21 14:46:45 UTC 2025 I: Submitting 8.0K b2/python-pdbfixer_1.9-5_arm64.buildinfo.asc https://buildinfo.debian.net/a8a0790df9ce681d9f974f5a8b5db214b3ae8f62/python-pdbfixer_1.9-5_all Tue Jan 21 14:47:02 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jan 21 14:47:02 UTC 2025 I: Done submitting .buildinfo files. Tue Jan 21 14:47:02 UTC 2025 I: Removing signed python-pdbfixer_1.9-5_arm64.buildinfo.asc files: removed './b1/python-pdbfixer_1.9-5_arm64.buildinfo.asc' removed './b2/python-pdbfixer_1.9-5_arm64.buildinfo.asc' 1737470822 arm64 unstable python-pdbfixer Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/python-pdbfixer_1.9-5.rbuild.log: 83.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/python-pdbfixer_1.9-5.rbuild.log.gz [2025-01-21 14:47:02] INFO: Starting at 2025-01-21 14:47:02.361599 [2025-01-21 14:47:02] INFO: Generating the pages of 1 package(s) [2025-01-21 14:47:02] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/python-pdbfixer_1.9-5.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/python-pdbfixer_1.9-5.diff.gz is missing [2025-01-21 14:47:02] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/python-pdbfixer_1.9-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/python-pdbfixer_1.9-4.diff.gz is missing [2025-01-21 14:47:02] 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 [2025-01-21 14:47:02] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/python-pdbfixer_1.8.1-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/python-pdbfixer_1.8.1-2.diff.gz is missing [2025-01-21 14:47:02] INFO: Finished at 2025-01-21 14:47:02.732477, took: 0:00:00.370883 All cleanup done. Tue Jan 21 14:47:02 UTC 2025 - total duration: 0h 4m 57s. Tue Jan 21 14:47:02 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-9q77hNMz, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 5min 40.257s CPU time consumed: 7.158s