Sun Nov 17 00:13:12 UTC 2024 I: starting to build python-pdbfixer/unstable/arm64 on jenkins on '2024-11-17 00:12' Sun Nov 17 00:13:12 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_5/68536/console.log Sun Nov 17 00:13:12 UTC 2024 I: Downloading source for unstable/python-pdbfixer=1.9-4 --2024-11-17 00:13:12-- http://deb.debian.org/debian/pool/main/p/python-pdbfixer/python-pdbfixer_1.9-4.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_1.9-4.dsc’ 0K .. 100% 334M=0s 2024-11-17 00:13:12 (334 MB/s) - ‘python-pdbfixer_1.9-4.dsc’ saved [2196/2196] Sun Nov 17 00:13:12 UTC 2024 I: python-pdbfixer_1.9-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-pdbfixer Binary: python3-pdbfixer Architecture: all Version: 1.9-4 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 bce855d281e398255ae822da6efefdb1a9d6375c 3032 python-pdbfixer_1.9-4.debian.tar.xz Checksums-Sha256: 88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb 648085 python-pdbfixer_1.9.orig.tar.gz 20e34a602494ab4b53d05330df4c3d8970fd5d4656492397f5711ef6f17ebd8a 3032 python-pdbfixer_1.9-4.debian.tar.xz Files: 48fc0c9c12eda19e786acbc9e62433f5 648085 python-pdbfixer_1.9.orig.tar.gz afcd8687f2c8a3c429f9bc025cfdf752 3032 python-pdbfixer_1.9-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEEj23hBDd/OxHnQXSHMfMURUShdBoFAmc4pUkRHHRjaGV0QGRl Ymlhbi5vcmcACgkQMfMURUShdBqb8A//QrBirRhPMEhSFlqTii5kcGi/PPXdVdeX qw/s0vjqmwEcqi6TNSZN1szl+OqN2wgBWGdsa2n8t0uVK7FMjAyvZTlCrF23Bg1W 4oqSivwDhAiEtPD/jwGqjx3RVmXjV/NNpTCElyu9zUgtc00HNww5jI2tl1BKTG3Y 7p51Id7b6eNHJ9/zfz/5GloIq6zMa9wtu/51Do9NqFeUMcanU5DwSbNFyWlZmd+H bxRgoTbQR9XvjMuOKhXtsoE4n3KXTHyr8eoX9J0X0LoEZPbQ6RVBqQI98AmV3qiK Y7hc0C5lqD+lN9NIgLdAyRDlux7U6eQ3dZ9MX46wwoY4Ni3fdSsI2s1os4i3MZl0 PrOLDx7bFqnhF5YNzGpsyLHPgCYtq0sogGSCuxJGb1+lKkPmTnsYj5nwI2Yz7qCK Urwr1dzTmmd/e9aUTCz+jg2XOSJb+Bhd1Y0F3Px4Wp7GLZyP4kQOXztneWm3t8Wf c7ie/am6xqJaveFwf0nS8TEyxcItMqejL1i6O47fPf/pQk4ruS0DspqQ2PE7oA6+ PcT8MyzzOxJwGNx56FHzGEcj0aeHmhNUqO1XiTL7RYrWXlAYpQA+3uP6Q3EIAdx6 s7A9F9TtGyMYHMcOMv67V4zQhrwGtinylUTZpkxQm59kn6QazzzKw5ebqOHKenq3 wfW8aPIz5nA= =2tt0 -----END PGP SIGNATURE----- Sun Nov 17 00:13:12 UTC 2024 I: Checking whether the package is not for us Sun Nov 17 00:13:12 UTC 2024 I: Starting 1st build on remote node codethink03-arm64.debian.net. Sun Nov 17 00:13:12 UTC 2024 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Sun Nov 17 00:14:16 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Dec 19 18:36:14 -12 2025 I: pbuilder-time-stamp: 1766212574 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_1.9-4.dsc] I: copying [./python-pdbfixer_1.9.orig.tar.gz] I: copying [./python-pdbfixer_1.9-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 16 13:59:37 2024 gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A gpgv: issuer "tchet@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-pdbfixer_1.9-4.dsc: no acceptable signature found dpkg-source: info: extracting python-pdbfixer in python-pdbfixer-1.9 dpkg-source: info: unpacking python-pdbfixer_1.9.orig.tar.gz dpkg-source: info: unpacking python-pdbfixer_1.9-4.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/128505/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='657f06a452554e608086c999b58b111f' 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='128505' 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.2ti1DzaU/pbuilderrc_FHUx --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.2ti1DzaU/b1 --logfile b1/build.log python-pdbfixer_1.9-4.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 codethink03-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/128505/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 ... 20084 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} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libopenmm-dev{a} libopenmm8.1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{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} python3.12{a} python3.12-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 krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-pygments wget 0 packages upgraded, 78 newly installed, 0 to remove and 0 not upgraded. Need to get 42.1 MB of archives. After unpacking 244 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 libpython3.12-minimal arm64 3.12.7-3 [808 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 python3.12-minimal arm64 3.12.7-3 [1940 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.7-1 [26.8 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 2024b-3 [255 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 13 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.7-3 [1902 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.7-3 [671 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.7-1 [9708 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.7-1 [27.8 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.2.0-1 [731 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20241024 [109 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-3+b1 [98.9 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-3+b1 [1812 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libopenmm8.1 arm64 8.1.2+dfsg-1+b1 [921 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libopenmm-dev arm64 8.1.2+dfsg-1+b1 [330 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 72 http://deb.debian.org/debian unstable/main arm64 python3-legacy-cgi all 2.6.1-2 [16.1 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 python3-openmm arm64 8.1.2+dfsg-1+b1 [6714 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 rename all 2.02-1 [21.8 kB] Fetched 42.1 MB in 1s (75.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 20084 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 libpython3.12-minimal:arm64. Preparing to unpack .../libpython3.12-minimal_3.12.7-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.7-3) ... 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 python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_arm64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:arm64 (3.12.7-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 20419 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_arm64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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Unpacking python3-numpy (1:1.26.4+ds-12) ... Selecting previously unselected package python3-openmm. Preparing to unpack .../51-python3-openmm_8.1.2+dfsg-1+b1_arm64.deb ... Unpacking python3-openmm (8.1.2+dfsg-1+b1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../52-python3-packaging_24.2-1_all.deb ... Unpacking python3-packaging (24.2-1) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../53-python3-pluggy_1.5.0-1_all.deb ... Unpacking python3-pluggy (1.5.0-1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../54-python3-pytest_8.3.3-1_all.deb ... Unpacking python3-pytest (8.3.3-1) ... Selecting previously unselected package rename. Preparing to unpack .../55-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 libkeyutils1:arm64 (1.6.3-4) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up rename (2.02-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up libcom-err2:arm64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Dec 20 06:36:42 UTC 2025. Universal Time is now: Sat Dec 20 06:36:42 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-3+b1) ... 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 autopoint (0.22.5-2) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libgfortran5:arm64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... 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 libkrb5-3:arm64 (1.21.3-3) ... Setting up libopenmm8.1 (8.1.2+dfsg-1+b1) ... Setting up readline-common (8.2-5) ... 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 (3.12.0-3+b1) ... 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 (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up libopenmm-dev (8.1.2+dfsg-1+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up libpython3.12-stdlib:arm64 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libpython3-stdlib:arm64 (3.12.7-1) ... Setting up python3 (3.12.7-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-packaging (24.2-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-legacy-cgi (2.6.1-2) ... Setting up python3-more-itertools (10.5.0-1) ... 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 (8.3.3-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-openmm (8.1.2+dfsg-1+b1) ... /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 dh-python (6.20241024) ... Processing triggers for libc-bin (2.40-3) ... 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_1.9-4_source.changes dpkg-buildpackage: info: source package python-pdbfixer dpkg-buildpackage: info: source version 1.9-4 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 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' dh_auto_clean I: pybuild base:311: python3.12 setup.py clean running clean removing '/build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it 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: python3.12 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_3.12_pdbfixer/build/pdbfixer copying pdbfixer/uiserver.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer copying pdbfixer/ui.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer copying pdbfixer/pdbfixer.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer copying pdbfixer/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/HIDE_test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/HIDE_test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/HIDE_test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/test_removechains.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests copying pdbfixer/soft.xml -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests/data copying pdbfixer/tests/data/test.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests/data copying pdbfixer/tests/data/4JSV.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests/data creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/VAL.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/U.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/TYR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/TRP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/THR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/SER.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/PRO.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/PHE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/NME.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/MET.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/LYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/LEU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ILE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/HIS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/GLY.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/GLU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/GLN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/G.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DT.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DC.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/DA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/CYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/C.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ASP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ASN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ARG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ALA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/ACE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates copying pdbfixer/templates/A.pdb -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/images copying pdbfixer/images/logo_small.png -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/images copying pdbfixer/images/logo.svg -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/images copying pdbfixer/images/logo.png -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/images copying pdbfixer/images/background.jpg -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/images creating /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html copying pdbfixer/html/start.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html copying pdbfixer/html/saveFile.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html copying pdbfixer/html/removeChains.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html copying pdbfixer/html/quit.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html copying pdbfixer/html/header.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html copying pdbfixer/html/error.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html copying pdbfixer/html/convertResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html copying pdbfixer/html/addResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html copying pdbfixer/html/addHydrogens.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html copying pdbfixer/html/addHeavyAtoms.html -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_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_3.12_pdbfixer/build; python3.12 -m pytest ============================= test session starts ============================== platform linux -- Python 3.12.7, pytest-8.3.3, 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_3.12_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 9.79s ========================= 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_3.12_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests copying pdbfixer/tests/test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests running install_lib creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/__pycache__/pdbfixer.cpython-312.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/__pycache__ creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html/addHeavyAtoms.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html/addHydrogens.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html/addResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html/convertResidues.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html/error.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html/header.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html/quit.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html/removeChains.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html/saveFile.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/html copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/html/start.html -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/html creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/images/background.jpg -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/images/logo.png -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/images/logo.svg -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/images copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/images/logo_small.png -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/images creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/A.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/ACE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/ALA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/ARG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/ASN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/ASP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/C.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/CYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/DA.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/DC.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/DG.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/DT.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/G.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/GLN.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/GLU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/GLY.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/HIS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/ILE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/LEU.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/LYS.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/MET.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/NME.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/PHE.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/PRO.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/SER.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/THR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/TRP.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/TYR.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/U.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/templates/VAL.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/templates copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/soft.xml -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests/test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests/test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests/test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests/__pycache__/test_removechains.cpython-312-pytest-8.3.3.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests/__pycache__ copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests/__pycache__ creating /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests/data copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests/data/4JSV.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests/data copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests/data/test.pdb -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests/data copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests/test_removechains.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests/HIDE_test_build_and_simulate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests/HIDE_test_cli.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/tests/HIDE_test_mutate.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/__init__.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/pdbfixer.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/ui.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer copying /build/reproducible-path/python-pdbfixer-1.9/.pybuild/cpython3_3.12_pdbfixer/build/pdbfixer/uiserver.py -> /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests/test_build_and_simulate.py to test_build_and_simulate.cpython-312.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests/test_cli.py to test_cli.cpython-312.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests/test_mutate.py to test_mutate.cpython-312.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests/test_removechains.py to test_removechains.cpython-312.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests/HIDE_test_build_and_simulate.py to HIDE_test_build_and_simulate.cpython-312.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests/HIDE_test_cli.py to HIDE_test_cli.cpython-312.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/tests/HIDE_test_mutate.py to HIDE_test_mutate.cpython-312.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/pdbfixer.py to pdbfixer.cpython-312.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/ui.py to ui.cpython-312.pyc byte-compiling /build/reproducible-path/python-pdbfixer-1.9/debian/python3-pdbfixer/usr/lib/python3.12/dist-packages/pdbfixer/uiserver.py to uiserver.cpython-312.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/python3.12/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' debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/python-pdbfixer-1.9' dh_python3 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_1.9-4_all.deb'. dpkg-genbuildinfo --build=binary -O../python-pdbfixer_1.9-4_arm64.buildinfo dpkg-genchanges --build=binary -O../python-pdbfixer_1.9-4_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/128505 and its subdirectories I: Current time: Fri Dec 19 18:37:14 -12 2025 I: pbuilder-time-stamp: 1766212634 Sun Nov 17 00:14:17 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net. Sun Nov 17 00:14:17 UTC 2024 I: Preparing to do remote build '2' on codethink01-arm64.debian.net. Sun Nov 17 00:15:42 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. Sun Nov 17 00:15:43 UTC 2024 I: python-pdbfixer_1.9-4_arm64.changes: Format: 1.8 Date: Sat, 16 Nov 2024 02:02:26 +0100 Source: python-pdbfixer Binary: python3-pdbfixer Architecture: all Version: 1.9-4 Distribution: unstable Urgency: medium Maintainer: Debian Python Team Changed-By: Alexandre Detiste Description: python3-pdbfixer - Fix problems in Protein Data Bank files (Python 3) Closes: 1084617 Changes: python-pdbfixer (1.9-4) unstable; urgency=medium . * Team Upload * Use dh-sequence-python3 * Add dep on python3-legacy-cgi (Closes: #1084617) Checksums-Sha1: 2014240cd2f5b9a3287c50868199a127fb20d71d 6281 python-pdbfixer_1.9-4_arm64.buildinfo f97583588d985a90ffa2ba3d1c723f12301bddab 436888 python3-pdbfixer_1.9-4_all.deb Checksums-Sha256: 461b59cda602c6d78c8c5eada99e10703af53b0dbd06f99480cabcab08ff6553 6281 python-pdbfixer_1.9-4_arm64.buildinfo 4196468221a6cb13a9b8efdde278c8f3ac9bdb487e06022a6951197e6c2cba17 436888 python3-pdbfixer_1.9-4_all.deb Files: 466414e4a6998ad99b7ea51ae57c643e 6281 python optional python-pdbfixer_1.9-4_arm64.buildinfo 6284dc0abf05c7296a719d8c3e37acc5 436888 python optional python3-pdbfixer_1.9-4_all.deb Sun Nov 17 00:15:44 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_5-68536.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.2ti1DzaU/python-pdbfixer_1.9-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.2ti1DzaU/python-pdbfixer_1.9-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.2ti1DzaU/python-pdbfixer_1.9-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.2ti1DzaU/b1/python-pdbfixer_1.9-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.2ti1DzaU/b2/python-pdbfixer_1.9-4_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: 0.354s) 0.354s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.019s) 0.019s 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: 667ms CPU time consumed: 668ms Sun Nov 17 00:15:45 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Sun Nov 17 00:15:45 UTC 2024 I: python-pdbfixer from unstable built successfully and reproducibly on arm64. Sun Nov 17 00:15:47 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Nov 17 00:15:47 UTC 2024 I: Submitting 8.0K b1/python-pdbfixer_1.9-4_arm64.buildinfo.asc Sun Nov 17 00:15:47 UTC 2024 I: Submitting 8.0K b2/python-pdbfixer_1.9-4_arm64.buildinfo.asc Sun Nov 17 00:15:48 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Nov 17 00:15:48 UTC 2024 I: Done submitting .buildinfo files. Sun Nov 17 00:15:48 UTC 2024 I: Removing signed python-pdbfixer_1.9-4_arm64.buildinfo.asc files: removed './b1/python-pdbfixer_1.9-4_arm64.buildinfo.asc' removed './b2/python-pdbfixer_1.9-4_arm64.buildinfo.asc'