Diff of the two buildlogs: -- --- b1/build.log 2024-05-16 17:22:40.835698050 +0000 +++ b2/build.log 2024-05-16 17:25:27.576603686 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 16 05:09:15 -12 2024 -I: pbuilder-time-stamp: 1715879355 +I: Current time: Thu Jun 19 13:45:43 +14 2025 +I: pbuilder-time-stamp: 1750290343 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying unversioned_docutils.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4075725/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1813756/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 18 23:45 /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/1813756/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1813756/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='12c01aa380994172b99c1c5131dba98b' - 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='4075725' - PS1='# ' - PS2='> ' + INVOCATION_ID=575039b736514741a9015fc5769e0435 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1813756 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.hnxC3IXL/pbuilderrc_NHJ1 --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.hnxC3IXL/b1 --logfile b1/build.log pdb2pqr_3.6.1+dfsg-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.hnxC3IXL/pbuilderrc_cDrD --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.hnxC3IXL/b2 --logfile b2/build.log pdb2pqr_3.6.1+dfsg-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 15 07:43 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4075725/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 17 14:07 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1813756/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -238,7 +270,7 @@ Get: 103 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 104 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-rtd-theme all 2.0.0+dfsg-1 [28.3 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 python3-testfixtures all 8.2.0-1 [86.4 kB] -Fetched 70.3 MB in 1s (50.9 MB/s) +Fetched 70.3 MB in 1s (88.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package fonts-lato. (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 ... 19701 files and directories currently installed.) @@ -583,8 +615,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu May 16 17:11:56 UTC 2024. -Universal Time is now: Thu May 16 17:11:56 UTC 2024. +Local time is now: Wed Jun 18 23:46:19 UTC 2025. +Universal Time is now: Wed Jun 18 23:46:19 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -697,7 +729,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/pdb2pqr-3.6.1+dfsg/ && 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 > ../pdb2pqr_3.6.1+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/1813756/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1813756/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/pdb2pqr-3.6.1+dfsg/ && 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 > ../pdb2pqr_3.6.1+dfsg-1_source.changes dpkg-buildpackage: info: source package pdb2pqr dpkg-buildpackage: info: source version 3.6.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -732,62 +768,62 @@ running build running build_py creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/pdb.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/definitions.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/cif.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/psize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/quatfit.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/na.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/utilities.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/cells.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/debump.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/config.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/forcefield.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/aa.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/main.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/_version.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/config.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/io.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/__main__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/aa.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/cells.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/psize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/definitions.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/pdb.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/biomolecule.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/residue.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/inputgen.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/_version.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/quatfit.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/cif.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/main.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/run.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens -copying pdb2pqr/hydrogens/optimize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens -copying pdb2pqr/hydrogens/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens -copying pdb2pqr/hydrogens/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens +copying pdb2pqr/residue.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/utilities.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/forcefield.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/debump.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/na.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/__main__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand -copying pdb2pqr/ligand/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand -copying pdb2pqr/ligand/mol2.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand copying pdb2pqr/ligand/peoe.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand copying pdb2pqr/ligand/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand +copying pdb2pqr/ligand/mol2.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand +copying pdb2pqr/ligand/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand +creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens +copying pdb2pqr/hydrogens/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens +copying pdb2pqr/hydrogens/optimize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens +copying pdb2pqr/hydrogens/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/AA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/PATCHES.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat -copying pdb2pqr/dat/TOPOLOGY.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat -copying pdb2pqr/dat/HYDROGENS.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/NA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat +copying pdb2pqr/dat/HYDROGENS.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat +copying pdb2pqr/dat/TOPOLOGY.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat +copying pdb2pqr/dat/AMBER.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/PARSE.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/CHARMM.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/PEOEPB.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat -copying pdb2pqr/dat/AMBER.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/TYL06.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/SWANSON.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat +copying pdb2pqr/dat/PEOEPB.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/CHARMM.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/TYL06.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat -copying pdb2pqr/dat/AMBER.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat -copying pdb2pqr/dat/PARSE.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat -copying pdb2pqr/dat/PEOEPB.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/SWANSON.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat +copying pdb2pqr/dat/PARSE.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat +copying pdb2pqr/dat/AMBER.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat PYTHONPATH=. python3 -m sphinx -N -bhtml docs/source build/html Running Sphinx v7.2.6 WARNING: html_static_path entry '_static' does not exist loading intersphinx inventory from https://docs.python.org/3/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) +intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) [autosummary] generating autosummary for: api/aa.rst, api/biomolecule.rst, api/cells.rst, api/cif.rst, api/config.rst, api/debump.rst, api/definitions.rst, api/forcefield.rst, api/hydrogens.rst, api/index.rst, ..., formats/xml-names.rst, getting.rst, help.rst, index.rst, releases.rst, supporting.rst, using/algorithms.rst, using/examples.rst, using/index.rst, using/other-software.rst building [mo]: targets for 0 po files that are out of date writing output... @@ -825,258 +861,258 @@ ERROR regression_test:regression_test.py:173 Need to reinstate the --apbs-input test with a temporary directory as path collected 316 items -tests/core_test.py::test_short_pdb[7BNA] SKIPPED (not running tests ...) 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PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. -INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP +INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 XFAIL [ 66%] -tests/core_test.py::test_broken_backbone[2V75] +tests/core_test.py::test_broken_backbone[1EJG] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_broken_backbone_2V75_0/2V75.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_broken_backbone_1EJG_0/1EJG.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. -INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 +INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG XFAIL [ 66%] -tests/core_test.py::test_broken_backbone[1EJG] +tests/core_test.py::test_broken_backbone[3U7T] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_broken_backbone_1EJG_0/1EJG.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_broken_backbone_3U7T_0/3U7T.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. -INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG +INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T XFAIL [ 67%] -tests/core_test.py::test_broken_backbone[3U7T] +tests/core_test.py::test_broken_backbone[4MGP] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_broken_backbone_3U7T_0/3U7T.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_broken_backbone_4MGP_0/4MGP.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. -INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T +INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP XFAIL [ 67%] tests/core_test.py::test_protonated_terminals[C-terminal HID] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1112,7 +1148,7 @@ PASSED [ 67%] tests/core_test.py::test_cyclic_peptide[Cyclic peptide] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1142,32 +1178,32 @@ INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 68%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 68%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 68%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 68%] +tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 68%] tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 68%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 69%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 69%] -tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 69%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 70%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 70%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 70%] -tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 71%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 69%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 69%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 69%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 70%] +tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 70%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 70%] +tests/io_test.py::test_read_pqr[tests/data/1HPX_with-ph=7.00_titration_state_method=propka_ligand=LIG_1HPX_ff=AMBER.pqr] PASSED [ 71%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 71%] tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 71%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 71%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 72%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 72%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 72%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 73%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 73%] -tests/io_test.py::test_read_pqr[tests/data/1HPX_with-ph=7.00_titration_state_method=propka_ligand=LIG_1HPX_ff=AMBER.pqr] PASSED [ 73%] -tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 74%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 72%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 72%] +tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 72%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 73%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 73%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 73%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 74%] tests/io_test.py::test_read_qcd PASSED [ 74%] tests/io_test.py::test_dx2cube -------------------------------- live log call --------------------------------- INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... -INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-pbuilder1/pytest-0/test_dx2cube0/test.cube... -INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-pbuilder1/pytest-0/test_dx2cube0/test.cube... +INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-pbuilder2/pytest-0/test_dx2cube0/test.cube... +INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-pbuilder2/pytest-0/test_dx2cube0/test.cube... INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... INFO io_test:io_test.py:68 No differences found in output PASSED [ 74%] @@ -1345,7 +1381,7 @@ tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] tests/regression_test.py::test_basic[1AFS basic local] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_basic_1AFS_basic_local_0/output.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_basic_1AFS_basic_local_0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1399,7 +1435,7 @@ PASSED [ 95%] tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa0/output.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_forcefields_1AFS_whitespa0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1443,7 +1479,7 @@ PASSED [ 95%] tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa1/output.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_forcefields_1AFS_whitespa1/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1484,7 +1520,7 @@ PASSED [ 95%] tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa2/output.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_forcefields_1AFS_whitespa2/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1524,7 +1560,7 @@ PASSED [ 96%] tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa3/output.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_forcefields_1AFS_whitespa3/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1564,7 +1600,7 @@ PASSED [ 96%] tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa4/output.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_forcefields_1AFS_whitespa4/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1604,7 +1640,7 @@ PASSED [ 96%] tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa5/output.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_forcefields_1AFS_whitespa5/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1644,7 +1680,7 @@ PASSED [ 97%] tests/regression_test.py::test_other_options[1AFS whitespace clean] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_other_options_1AFS_whites0/output.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_other_options_1AFS_whites0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1664,7 +1700,7 @@ PASSED [ 97%] tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_other_options_1A1P_assign0/output.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_other_options_1A1P_assign0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1690,7 +1726,7 @@ PASSED [ 97%] tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_other_options_1A1P_nodebu0/output.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_other_options_1A1P_nodebu0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1721,7 +1757,7 @@ PASSED [ 98%] tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_other_options_1AFS_chain_0/output.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_other_options_1AFS_chain_0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1761,7 +1797,7 @@ PASSED [ 98%] tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_other_options_1AFS_neutra0/output.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_other_options_1AFS_neutra0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1801,7 +1837,7 @@ PASSED [ 98%] tests/regression_test.py::test_other_options[1AFS drop-water AMBER] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_other_options_1AFS_drop_w0/output.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_other_options_1AFS_drop_w0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1842,7 +1878,7 @@ PASSED [ 99%] tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] -------------------------------- live log call --------------------------------- -INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_other_options_1AFS_userff0/output.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_other_options_1AFS_userff0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). @@ -1883,7 +1919,7 @@ tests/test_version.py::test_version_exists PASSED [ 99%] tests/test_version.py::test_version PASSED [100%] -============ 92 passed, 220 skipped, 4 xfailed in 366.79s (0:06:06) ============ +============ 92 passed, 220 skipped, 4 xfailed in 66.13s (0:01:06) ============= create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -1911,124 +1947,124 @@ creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11 creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages -creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/.pytest_cache/.gitignore -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/.pytest_cache/README.md -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/.pytest_cache/CACHEDIR.TAG -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache -creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v -creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v/cache -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/.pytest_cache/v/cache/stepwise -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v/cache -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/.pytest_cache/v/cache/nodeids -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v/cache creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/pdb.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/CHARMM.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PATCHES.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TYL06.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AMBER.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PARSE.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/CHARMM.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PARSE.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PEOEPB.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PEOEPB.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AMBER.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TOPOLOGY.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/HYDROGENS.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TYL06.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/SWANSON.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/NA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/SWANSON.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/_version.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/config.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/io.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/aa.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/cells.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/psize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/definitions.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/peoe.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/mol2.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand +creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/mol2.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/peoe.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/pdb.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/biomolecule.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/inputgen.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/quatfit.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/cif.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/optimize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/optimize.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/optimize.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/structures.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/optimize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/main.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/run.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/inputgen.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/residue.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/cif.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/main.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/config.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/psize.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/io.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/pdb.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/cells.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/quatfit.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/definitions.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/utilities.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/debump.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/cif.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/_version.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/definitions.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/cells.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/na.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/aa.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/biomolecule.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/forcefield.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/structures.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/na.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/residue.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/psize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand -creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/peoe.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/mol2.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/mol2.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/peoe.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/quatfit.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/na.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/utilities.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/forcefield.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/psize.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/io.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/config.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/pdb.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/inputgen.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/debump.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/residue.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/utilities.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/cells.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/debump.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/config.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/forcefield.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/aa.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/main.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/io.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/debump.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/na.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__main__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/biomolecule.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/residue.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/inputgen.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/_version.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/run.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/pdb.py to pdb.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/definitions.py to definitions.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/cif.py to cif.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/optimize.py to optimize.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__init__.py to __init__.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/structures.py to structures.cpython-311.pyc +creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PATCHES.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PEOEPB.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/CHARMM.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AMBER.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TYL06.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PARSE.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/CHARMM.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/SWANSON.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/NA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PEOEPB.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PARSE.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TYL06.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AMBER.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/SWANSON.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/HYDROGENS.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TOPOLOGY.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache +creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v +creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v/cache +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/.pytest_cache/v/cache/nodeids -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v/cache +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/.pytest_cache/v/cache/stepwise -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v/cache +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/.pytest_cache/CACHEDIR.TAG -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/.pytest_cache/README.md -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache +copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/.pytest_cache/.gitignore -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/_version.py to _version.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/structures.py to structures.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/config.py to config.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/io.py to io.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/aa.py to aa.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/topology.py to topology.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/cells.py to cells.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/psize.py to psize.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__init__.py to __init__.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/mol2.py to mol2.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/definitions.py to definitions.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/peoe.py to peoe.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/topology.py to topology.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/quatfit.py to quatfit.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/na.py to na.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/utilities.py to utilities.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/cells.py to cells.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/debump.py to debump.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/mol2.py to mol2.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__init__.py to __init__.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/topology.py to topology.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/config.py to config.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/forcefield.py to forcefield.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/aa.py to aa.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/main.py to main.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/structures.py to structures.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/io.py to io.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__main__.py to __main__.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/pdb.py to pdb.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/biomolecule.py to biomolecule.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/residue.py to residue.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/inputgen.py to inputgen.cpython-311.pyc -byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/_version.py to _version.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/quatfit.py to quatfit.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/cif.py to cif.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/structures.py to structures.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/optimize.py to optimize.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__init__.py to __init__.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/main.py to main.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/run.py to run.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/residue.py to residue.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/utilities.py to utilities.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/forcefield.py to forcefield.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/debump.py to debump.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/na.py to na.cpython-311.pyc +byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__main__.py to __main__.cpython-311.pyc running install_egg_info running egg_info creating pdb2pqr.egg-info @@ -2090,12 +2126,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1813756/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1813756/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/4075725 and its subdirectories -I: Current time: Thu May 16 05:22:40 -12 2024 -I: pbuilder-time-stamp: 1715880160 +I: removing directory /srv/workspace/pbuilder/1813756 and its subdirectories +I: Current time: Thu Jun 19 13:48:26 +14 2025 +I: pbuilder-time-stamp: 1750290506