Diff of the two buildlogs: -- --- b1/build.log 2023-06-06 12:32:57.473224957 +0000 +++ b2/build.log 2023-06-06 12:38:42.990091979 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jul 8 06:53:46 -12 2024 -I: pbuilder-time-stamp: 1720464826 +I: Current time: Wed Jun 7 02:32:59 +14 2023 +I: pbuilder-time-stamp: 1686054779 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./pdb2pqr_3.5.2+dfsg.orig.tar.xz] I: copying [./pdb2pqr_3.5.2+dfsg-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Feb 4 20:07:43 2023 -12 +gpgv: Signature made Sun Feb 5 22:07:43 2023 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,137 +30,169 @@ 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/49292/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/11680/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +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 7 02:33 /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/11680/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/11680/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='i386' + 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]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='bae00b8c1ed04dba82d4fa99cc745bde' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='49292' - PS1='# ' - PS2='> ' + INVOCATION_ID=0c392963a67b4b4abd1f0acd49dc46a2 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=11680 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.bKBR9kUt/pbuilderrc_uiII --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bKBR9kUt/b1 --logfile b1/build.log pdb2pqr_3.5.2+dfsg-3.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.bKBR9kUt/pbuilderrc_JxgP --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bKBR9kUt/b2 --logfile b2/build.log --extrapackages usrmerge pdb2pqr_3.5.2+dfsg-3.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos6-i386 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-686-pae #1 SMP Debian 5.10.179-1 (2023-05-12) i686 GNU/Linux I: ls -l /bin total 6036 - -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown - -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp - -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash - -rwxr-xr-x 1 root root 137160 Sep 20 2022 date - -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd - -rwxr-xr-x 1 root root 108940 Sep 20 2022 df - -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir - -rwxr-xr-x 1 root root 87760 Mar 22 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 34664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln - -rwxr-xr-x 1 root root 55600 Mar 22 2023 login - -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls - -rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 63016 Mar 22 2023 more - -rwsr-xr-x 1 root root 58912 Mar 22 2023 mount - -rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash - -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm - -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty - -rwsr-xr-x 1 root root 83492 Mar 22 2023 su - -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync - -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar - -rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch - -rwxr-xr-x 1 root root 34664 Sep 20 2022 true - -rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Mar 22 2023 umount - -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 71216 Mar 22 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/49292/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1408088 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown + -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp + -rwxr-xr-x 1 root root 136916 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 137160 Sep 21 2022 date + -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd + -rwxr-xr-x 1 root root 108940 Sep 21 2022 df + -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir + -rwxr-xr-x 1 root root 87760 Mar 24 00:20 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 34664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 84272 Mar 24 00:20 findmnt + -rwsr-xr-x 1 root root 30240 Mar 23 22:38 fusermount + -rwxr-xr-x 1 root root 218680 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 21916 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln + -rwxr-xr-x 1 root root 55600 Mar 24 01:43 login + -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls + -rwxr-xr-x 1 root root 214568 Mar 24 00:20 lsblk + -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 63016 Mar 24 00:20 more + -rwsr-xr-x 1 root root 58912 Mar 24 00:20 mount + -rwxr-xr-x 1 root root 13856 Mar 24 00:20 mountpoint + -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm + -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133224 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Jun 7 02:33 sh -> /bin/bash + -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty + -rwsr-xr-x 1 root root 83492 Mar 24 00:20 su + -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync + -rwxr-xr-x 1 root root 598456 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch + -rwxr-xr-x 1 root root 34664 Sep 21 2022 true + -rwxr-xr-x 1 root root 17892 Mar 23 22:38 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Mar 24 00:20 umount + -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 71216 Mar 24 00:20 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/11680/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -325,7 +357,7 @@ Get: 103 http://deb.debian.org/debian bookworm/main i386 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB] Get: 104 http://deb.debian.org/debian bookworm/main i386 python3-sphinx-rtd-theme all 1.2.0+dfsg-1 [27.7 kB] Get: 105 http://deb.debian.org/debian bookworm/main i386 python3-testfixtures all 7.0.4-1 [79.8 kB] -Fetched 66.3 MB in 1s (95.4 MB/s) +Fetched 66.3 MB in 1s (50.3 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 ... 19599 files and directories currently installed.) @@ -773,8 +805,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/pdb2pqr-3.5.2+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_3.5.2+dfsg-3_source.changes +I: user script /srv/workspace/pbuilder/11680/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/11680/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/pdb2pqr-3.5.2+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_3.5.2+dfsg-3_source.changes dpkg-buildpackage: info: source package pdb2pqr dpkg-buildpackage: info: source version 3.5.2+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -809,55 +852,55 @@ running build running build_py creating /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/run.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/inputgen.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/aa.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/debump.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/definitions.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/main.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/io.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/topology.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/psize.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/cif.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/_version.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/forcefield.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/aa.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/na.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/__main__.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/psize.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/structures.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/cells.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/residue.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/config.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/biomolecule.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/definitions.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/pdb.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/main.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/_version.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/residue.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/forcefield.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/run.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/__main__.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/cif.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/utilities.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/pdb.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -copying pdb2pqr/io.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/quatfit.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr -creating /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand -copying pdb2pqr/ligand/topology.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand -copying pdb2pqr/ligand/peoe.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand -copying pdb2pqr/ligand/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand -copying pdb2pqr/ligand/mol2.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand +copying pdb2pqr/debump.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/biomolecule.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr +copying pdb2pqr/inputgen.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr creating /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens copying pdb2pqr/hydrogens/structures.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens copying pdb2pqr/hydrogens/optimize.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens copying pdb2pqr/hydrogens/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens +creating /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand +copying pdb2pqr/ligand/topology.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand +copying pdb2pqr/ligand/mol2.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand +copying pdb2pqr/ligand/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand +copying pdb2pqr/ligand/peoe.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand creating /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat -copying pdb2pqr/dat/TOPOLOGY.xml -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/AA.xml -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat +copying pdb2pqr/dat/HYDROGENS.xml -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat +copying pdb2pqr/dat/TOPOLOGY.xml -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/NA.xml -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/PATCHES.xml -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat -copying pdb2pqr/dat/HYDROGENS.xml -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat -copying pdb2pqr/dat/SWANSON.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat -copying pdb2pqr/dat/TYL06.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/PARSE.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat -copying pdb2pqr/dat/PEOEPB.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat +copying pdb2pqr/dat/SWANSON.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/AMBER.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/CHARMM.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat -copying pdb2pqr/dat/AMBER.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat +copying pdb2pqr/dat/PEOEPB.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat +copying pdb2pqr/dat/TYL06.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/CHARMM.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat +copying pdb2pqr/dat/PEOEPB.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/SWANSON.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat +copying pdb2pqr/dat/AMBER.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/TYL06.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat -copying pdb2pqr/dat/PEOEPB.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/PARSE.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat PYTHONPATH=. python3 -m sphinx -N -bhtml docs/source build/html Running Sphinx v5.3.0 @@ -865,7 +908,7 @@ 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 building [html]: targets for 39 source files that are out of date @@ -1003,228 +1046,228 @@ ERROR regression_test:regression_test.py:173 Need to reinstate the --apbs-input test with a temporary directory as path collected 307 items -tests/core_test.py::test_short_pdb[1K1I] SKIPPED (not running tests ...) [ 0%] -tests/core_test.py::test_short_pdb[1FAS] SKIPPED (not running tests ...) [ 0%] +tests/core_test.py::test_short_pdb[4UN3] SKIPPED (not running tests ...) [ 0%] +tests/core_test.py::test_short_pdb[7BNA] SKIPPED (not running tests ...) [ 0%] tests/core_test.py::test_short_pdb[1NAJ] SKIPPED (not running tests ...) [ 0%] -tests/core_test.py::test_short_pdb[4E8M] SKIPPED (not running tests ...) [ 1%] -tests/core_test.py::test_short_pdb[4UN3] SKIPPED (not running tests ...) [ 1%] +tests/core_test.py::test_short_pdb[1K1I] SKIPPED (not running tests ...) [ 1%] tests/core_test.py::test_short_pdb[1AQO] SKIPPED (not running tests ...) [ 1%] -tests/core_test.py::test_short_pdb[7BNA] SKIPPED (not running tests ...) [ 2%] +tests/core_test.py::test_short_pdb[1FAS] SKIPPED (not running tests ...) [ 1%] +tests/core_test.py::test_short_pdb[4E8M] SKIPPED (not running tests ...) [ 2%] tests/core_test.py::test_short_pdb[5D8V] SKIPPED (not running tests ...) [ 2%] -tests/core_test.py::test_basic_cif[1K1I] SKIPPED (not running tests ...) [ 2%] -tests/core_test.py::test_basic_cif[1FAS] SKIPPED (not running tests ...) [ 3%] +tests/core_test.py::test_basic_cif[4UN3] SKIPPED (not running tests ...) [ 2%] +tests/core_test.py::test_basic_cif[7BNA] SKIPPED (not running tests ...) [ 3%] tests/core_test.py::test_basic_cif[1NAJ] SKIPPED (not running tests ...) [ 3%] -tests/core_test.py::test_basic_cif[4E8M] SKIPPED (not running tests ...) [ 3%] -tests/core_test.py::test_basic_cif[4UN3] SKIPPED (not running tests ...) [ 4%] +tests/core_test.py::test_basic_cif[1K1I] SKIPPED (not running tests ...) [ 3%] tests/core_test.py::test_basic_cif[1AQO] SKIPPED (not running tests ...) [ 4%] -tests/core_test.py::test_basic_cif[7BNA] SKIPPED (not running tests ...) [ 4%] +tests/core_test.py::test_basic_cif[1FAS] SKIPPED (not running tests ...) [ 4%] +tests/core_test.py::test_basic_cif[4E8M] SKIPPED (not running tests ...) [ 4%] tests/core_test.py::test_basic_cif[5D8V] SKIPPED (not running tests ...) [ 5%] -tests/core_test.py::test_long_pdb[1X3O] SKIPPED (not running tests r...) [ 5%] -tests/core_test.py::test_long_pdb[2XXC] SKIPPED (not running tests r...) [ 5%] -tests/core_test.py::test_long_pdb[3ISU] SKIPPED (not running tests r...) [ 6%] -tests/core_test.py::test_long_pdb[4I2T] SKIPPED (not running tests r...) [ 6%] -tests/core_test.py::test_long_pdb[3QE1] SKIPPED (not running tests r...) [ 6%] -tests/core_test.py::test_long_pdb[3LMO] SKIPPED (not running tests r...) [ 7%] -tests/core_test.py::test_long_pdb[1FAS] SKIPPED (not running tests r...) [ 7%] -tests/core_test.py::test_long_pdb[2FI9] SKIPPED (not running tests r...) [ 7%] -tests/core_test.py::test_long_pdb[1IS5] SKIPPED (not running tests r...) [ 8%] -tests/core_test.py::test_long_pdb[1YZM] SKIPPED (not running tests r...) [ 8%] -tests/core_test.py::test_long_pdb[2PMR] SKIPPED (not running tests r...) [ 8%] -tests/core_test.py::test_long_pdb[4HS2] SKIPPED (not running tests r...) [ 9%] -tests/core_test.py::test_long_pdb[3CSR] SKIPPED (not running tests r...) [ 9%] -tests/core_test.py::test_long_pdb[3ZZP] SKIPPED (not running tests r...) [ 9%] -tests/core_test.py::test_long_pdb[2ERW] SKIPPED (not running tests r...) [ 10%] -tests/core_test.py::test_long_pdb[2QBV] SKIPPED (not running tests r...) [ 10%] -tests/core_test.py::test_long_pdb[2EBB] SKIPPED (not running tests r...) [ 10%] -tests/core_test.py::test_long_pdb[3US6] SKIPPED (not running tests r...) [ 11%] -tests/core_test.py::test_long_pdb[3HRN] SKIPPED (not running tests r...) [ 11%] -tests/core_test.py::test_long_pdb[3QC7] SKIPPED (not running tests r...) [ 11%] -tests/core_test.py::test_long_pdb[1P9I] SKIPPED (not running tests r...) [ 12%] -tests/core_test.py::test_long_pdb[1USE] SKIPPED (not running tests r...) [ 12%] -tests/core_test.py::test_long_pdb[2SGA] SKIPPED (not running tests r...) [ 12%] -tests/core_test.py::test_long_pdb[1YIB] SKIPPED (not running tests r...) [ 13%] -tests/core_test.py::test_long_pdb[2D8E] SKIPPED (not running tests r...) [ 13%] -tests/core_test.py::test_long_pdb[1OPS] SKIPPED (not running tests r...) [ 13%] +tests/core_test.py::test_long_pdb[1ZZK] SKIPPED (not running tests r...) [ 5%] +tests/core_test.py::test_long_pdb[1L2P] SKIPPED (not running tests r...) [ 5%] +tests/core_test.py::test_long_pdb[3ZZP] SKIPPED (not running tests r...) [ 6%] +tests/core_test.py::test_long_pdb[2OO2] SKIPPED (not running tests r...) [ 6%] +tests/core_test.py::test_long_pdb[2J9V] SKIPPED (not running tests r...) [ 6%] +tests/core_test.py::test_long_pdb[4O7Q] SKIPPED (not running tests r...) [ 7%] +tests/core_test.py::test_long_pdb[3TSV] SKIPPED (not running tests r...) [ 7%] +tests/core_test.py::test_long_pdb[2TGI] SKIPPED (not running tests r...) [ 7%] +tests/core_test.py::test_long_pdb[2CMP] SKIPPED (not running tests r...) [ 8%] +tests/core_test.py::test_long_pdb[2J70] SKIPPED (not running tests r...) [ 8%] +tests/core_test.py::test_long_pdb[1SJV] SKIPPED (not running tests r...) [ 8%] +tests/core_test.py::test_long_pdb[3HRN] SKIPPED (not running tests r...) [ 9%] +tests/core_test.py::test_long_pdb[2FWG] SKIPPED (not running tests r...) [ 9%] +tests/core_test.py::test_long_pdb[2NWD] SKIPPED (not running tests r...) [ 9%] +tests/core_test.py::test_long_pdb[4GS3] SKIPPED (not running tests r...) [ 10%] +tests/core_test.py::test_long_pdb[2ZQE] SKIPPED (not running tests r...) [ 10%] +tests/core_test.py::test_long_pdb[1XAK] SKIPPED (not running tests r...) [ 10%] +tests/core_test.py::test_long_pdb[3FH2] SKIPPED (not running tests r...) [ 11%] +tests/core_test.py::test_long_pdb[5EE2] SKIPPED (not running tests r...) [ 11%] +tests/core_test.py::test_long_pdb[1BM8] SKIPPED (not running tests r...) [ 11%] +tests/core_test.py::test_long_pdb[1HOE] SKIPPED (not running tests r...) [ 12%] +tests/core_test.py::test_long_pdb[3CQT] SKIPPED (not running tests r...) [ 12%] +tests/core_test.py::test_long_pdb[1PZC] SKIPPED (not running tests r...) [ 12%] +tests/core_test.py::test_long_pdb[2CJJ] SKIPPED (not running tests r...) [ 13%] +tests/core_test.py::test_long_pdb[1DUP] SKIPPED (not running tests r...) [ 13%] +tests/core_test.py::test_long_pdb[1LN4] SKIPPED (not running tests r...) [ 13%] tests/core_test.py::test_long_pdb[2G7O] SKIPPED (not running tests r...) [ 14%] -tests/core_test.py::test_long_pdb[2IBL] SKIPPED (not running tests r...) [ 14%] -tests/core_test.py::test_long_pdb[3SO2] SKIPPED (not running tests r...) [ 14%] -tests/core_test.py::test_long_pdb[1TIG] SKIPPED (not running tests r...) [ 14%] -tests/core_test.py::test_long_pdb[3ONJ] SKIPPED (not running tests r...) [ 15%] +tests/core_test.py::test_long_pdb[1OX3] SKIPPED (not running tests r...) [ 14%] +tests/core_test.py::test_long_pdb[2QR3] SKIPPED (not running tests r...) [ 14%] +tests/core_test.py::test_long_pdb[1R5Q] SKIPPED (not running tests r...) [ 14%] tests/core_test.py::test_long_pdb[1UG4] SKIPPED (not running tests r...) [ 15%] -tests/core_test.py::test_long_pdb[1E7G] SKIPPED (not running tests r...) [ 15%] -tests/core_test.py::test_long_pdb[1Z0P] SKIPPED (not running tests r...) [ 16%] -tests/core_test.py::test_long_pdb[4Q2Q] SKIPPED (not running tests r...) [ 16%] -tests/core_test.py::test_long_pdb[2HC8] SKIPPED (not running tests r...) [ 16%] -tests/core_test.py::test_long_pdb[1R5Q] SKIPPED (not running tests r...) [ 17%] -tests/core_test.py::test_long_pdb[4TTW] SKIPPED (not running tests r...) [ 17%] -tests/core_test.py::test_long_pdb[4POY] SKIPPED (not running tests r...) [ 17%] -tests/core_test.py::test_long_pdb[1SJV] SKIPPED (not running tests r...) [ 18%] -tests/core_test.py::test_long_pdb[2OCH] SKIPPED (not running tests r...) [ 18%] -tests/core_test.py::test_long_pdb[3I35] SKIPPED (not running tests r...) [ 18%] -tests/core_test.py::test_long_pdb[1PGX] SKIPPED (not running tests r...) [ 19%] -tests/core_test.py::test_long_pdb[4S11] SKIPPED (not running tests r...) [ 19%] -tests/core_test.py::test_long_pdb[4NPN] SKIPPED (not running tests r...) [ 19%] -tests/core_test.py::test_long_pdb[1AIL] SKIPPED (not running tests r...) [ 20%] -tests/core_test.py::test_long_pdb[2FWG] SKIPPED (not running tests r...) [ 20%] -tests/core_test.py::test_long_pdb[3RJS] SKIPPED (not running tests r...) [ 20%] -tests/core_test.py::test_long_pdb[1ZX6] SKIPPED (not running tests r...) [ 21%] -tests/core_test.py::test_long_pdb[2J9V] SKIPPED (not running tests r...) [ 21%] -tests/core_test.py::test_long_pdb[3C97] SKIPPED (not running tests r...) [ 21%] -tests/core_test.py::test_long_pdb[1V2Z] SKIPPED (not running tests r...) [ 22%] -tests/core_test.py::test_long_pdb[4CRH] SKIPPED (not running tests r...) [ 22%] -tests/core_test.py::test_long_pdb[1YQB] SKIPPED (not running tests r...) [ 22%] -tests/core_test.py::test_long_pdb[1LN4] SKIPPED (not running tests r...) [ 23%] -tests/core_test.py::test_long_pdb[3ZHI] SKIPPED (not running tests r...) [ 23%] -tests/core_test.py::test_long_pdb[2GUS] SKIPPED (not running tests r...) [ 23%] -tests/core_test.py::test_long_pdb[4PGR] SKIPPED (not running tests r...) [ 24%] -tests/core_test.py::test_long_pdb[2OO2] SKIPPED (not running tests r...) [ 24%] -tests/core_test.py::test_long_pdb[2QR3] SKIPPED (not running tests r...) [ 24%] -tests/core_test.py::test_long_pdb[2HDZ] SKIPPED (not running tests r...) [ 25%] +tests/core_test.py::test_long_pdb[3C97] SKIPPED (not running tests r...) [ 15%] +tests/core_test.py::test_long_pdb[4AXT] SKIPPED (not running tests r...) [ 15%] +tests/core_test.py::test_long_pdb[2CWR] SKIPPED (not running tests r...) [ 16%] +tests/core_test.py::test_long_pdb[1X6J] SKIPPED (not running tests r...) [ 16%] +tests/core_test.py::test_long_pdb[3I35] SKIPPED (not running tests r...) [ 16%] +tests/core_test.py::test_long_pdb[3HRO] SKIPPED (not running tests r...) [ 17%] +tests/core_test.py::test_long_pdb[1AFS] SKIPPED (not running tests r...) [ 17%] +tests/core_test.py::test_long_pdb[2XXC] SKIPPED (not running tests r...) [ 17%] +tests/core_test.py::test_long_pdb[2D8E] SKIPPED (not running tests r...) [ 18%] +tests/core_test.py::test_long_pdb[4I2T] SKIPPED (not running tests r...) [ 18%] +tests/core_test.py::test_long_pdb[4PGR] SKIPPED (not running tests r...) [ 18%] +tests/core_test.py::test_long_pdb[2CKX] SKIPPED (not running tests r...) [ 19%] +tests/core_test.py::test_long_pdb[2PCY] SKIPPED (not running tests r...) [ 19%] +tests/core_test.py::test_long_pdb[2BYG] SKIPPED (not running tests r...) [ 19%] +tests/core_test.py::test_long_pdb[4N6T] SKIPPED (not running tests r...) [ 20%] +tests/core_test.py::test_long_pdb[2HDZ] SKIPPED (not running tests r...) [ 20%] +tests/core_test.py::test_long_pdb[1R7J] SKIPPED (not running tests r...) [ 20%] +tests/core_test.py::test_long_pdb[2H2C] SKIPPED (not running tests r...) [ 21%] +tests/core_test.py::test_long_pdb[4EO0] SKIPPED (not running tests r...) [ 21%] +tests/core_test.py::test_long_pdb[1V2Z] SKIPPED (not running tests r...) [ 21%] +tests/core_test.py::test_long_pdb[4L9E] SKIPPED (not running tests r...) [ 22%] +tests/core_test.py::test_long_pdb[2GUS] SKIPPED (not running tests r...) [ 22%] +tests/core_test.py::test_long_pdb[3V1A] SKIPPED (not running tests r...) [ 22%] +tests/core_test.py::test_long_pdb[1YZM] SKIPPED (not running tests r...) [ 23%] +tests/core_test.py::test_long_pdb[2REY] SKIPPED (not running tests r...) [ 23%] +tests/core_test.py::test_long_pdb[1P9I] SKIPPED (not running tests r...) [ 23%] +tests/core_test.py::test_long_pdb[2YXF] SKIPPED (not running tests r...) [ 24%] +tests/core_test.py::test_long_pdb[1ZLM] SKIPPED (not running tests r...) [ 24%] +tests/core_test.py::test_long_pdb[1FAS] SKIPPED (not running tests r...) [ 24%] +tests/core_test.py::test_long_pdb[4G3O] SKIPPED (not running tests r...) [ 25%] tests/core_test.py::test_long_pdb[2VWR] SKIPPED (not running tests r...) [ 25%] -tests/core_test.py::test_long_pdb[2NSN] SKIPPED (not running tests r...) [ 25%] -tests/core_test.py::test_long_pdb[2SFA] SKIPPED (not running tests r...) [ 26%] -tests/core_test.py::test_long_pdb[4CVD] SKIPPED (not running tests r...) [ 26%] -tests/core_test.py::test_long_pdb[2FRG] SKIPPED (not running tests r...) [ 26%] -tests/core_test.py::test_long_pdb[3LAA] SKIPPED (not running tests r...) [ 27%] -tests/core_test.py::test_long_pdb[4L9E] SKIPPED (not running tests r...) [ 27%] -tests/core_test.py::test_long_pdb[2PCY] SKIPPED (not running tests r...) [ 27%] -tests/core_test.py::test_long_pdb[4GS3] SKIPPED (not running tests r...) [ 28%] -tests/core_test.py::test_long_pdb[2FD4] SKIPPED (not running tests r...) [ 28%] -tests/core_test.py::test_long_pdb[4YPC] SKIPPED (not running tests r...) [ 28%] -tests/core_test.py::test_long_pdb[2PTV] SKIPPED (not running tests r...) [ 28%] -tests/core_test.py::test_long_pdb[1JQ0] SKIPPED (not running tests r...) [ 29%] -tests/core_test.py::test_long_pdb[4RWU] SKIPPED (not running tests r...) [ 29%] -tests/core_test.py::test_long_pdb[1ZLM] SKIPPED (not running tests r...) [ 29%] -tests/core_test.py::test_long_pdb[2OP6] SKIPPED (not running tests r...) [ 30%] -tests/core_test.py::test_long_pdb[2J6B] SKIPPED (not running tests r...) [ 30%] -tests/core_test.py::test_long_pdb[3IDW] SKIPPED (not running tests r...) [ 30%] -tests/core_test.py::test_long_pdb[2NWD] SKIPPED (not running tests r...) [ 31%] -tests/core_test.py::test_long_pdb[4IL7] SKIPPED (not running tests r...) [ 31%] -tests/core_test.py::test_long_pdb[4G3O] SKIPPED (not running tests r...) [ 31%] -tests/core_test.py::test_long_pdb[5DV8] SKIPPED (not running tests r...) [ 32%] -tests/core_test.py::test_long_pdb[1RJ1] SKIPPED (not running tests r...) [ 32%] -tests/core_test.py::test_long_pdb[1PDO] SKIPPED (not running tests r...) [ 32%] -tests/core_test.py::test_long_pdb[1ZZK] SKIPPED (not running tests r...) [ 33%] -tests/core_test.py::test_long_pdb[1BM8] SKIPPED (not running tests r...) [ 33%] -tests/core_test.py::test_long_pdb[3S0A] SKIPPED (not running tests r...) [ 33%] -tests/core_test.py::test_long_pdb[2PND] SKIPPED (not running tests r...) [ 34%] -tests/core_test.py::test_long_pdb[3NX6] SKIPPED (not running tests r...) [ 34%] -tests/core_test.py::test_long_pdb[3KT2] SKIPPED (not running tests r...) [ 34%] -tests/core_test.py::test_long_pdb[4GQM] SKIPPED (not running tests r...) [ 35%] -tests/core_test.py::test_long_pdb[4HTI] SKIPPED (not running tests r...) [ 35%] -tests/core_test.py::test_long_pdb[2J70] SKIPPED (not running tests r...) [ 35%] -tests/core_test.py::test_long_pdb[4EO0] SKIPPED (not running tests r...) [ 36%] -tests/core_test.py::test_long_pdb[4AXT] SKIPPED (not running tests r...) [ 36%] -tests/core_test.py::test_long_pdb[2QVO] SKIPPED (not running tests r...) [ 36%] -tests/core_test.py::test_long_pdb[4N6T] SKIPPED (not running tests r...) [ 37%] -tests/core_test.py::test_long_pdb[1AFS] SKIPPED (not running tests r...) [ 37%] -tests/core_test.py::test_long_pdb[2IWN] SKIPPED (not running tests r...) [ 37%] -tests/core_test.py::test_long_pdb[3KZD] SKIPPED (not running tests r...) [ 38%] -tests/core_test.py::test_long_pdb[2HP7] SKIPPED (not running tests r...) [ 38%] -tests/core_test.py::test_long_pdb[1X6J] SKIPPED (not running tests r...) [ 38%] -tests/core_test.py::test_long_pdb[1TGN] SKIPPED (not running tests r...) [ 39%] -tests/core_test.py::test_long_pdb[3T8R] SKIPPED (not running tests r...) [ 39%] -tests/core_test.py::test_long_pdb[2GZV] SKIPPED (not running tests r...) [ 39%] -tests/core_test.py::test_long_pdb[1DUP] SKIPPED (not running tests r...) [ 40%] -tests/core_test.py::test_long_pdb[3CP1] SKIPPED (not running tests r...) [ 40%] -tests/core_test.py::test_long_pdb[4O7Q] SKIPPED (not running tests r...) [ 40%] -tests/core_test.py::test_long_pdb[2JCP] SKIPPED (not running tests r...) [ 41%] -tests/core_test.py::test_long_pdb[3CE7] SKIPPED (not running tests r...) [ 41%] -tests/core_test.py::test_long_pdb[1ZVA] SKIPPED (not running tests r...) [ 41%] -tests/core_test.py::test_long_pdb[3T1S] SKIPPED (not running tests r...) [ 42%] -tests/core_test.py::test_long_pdb[4ZQA] SKIPPED (not running tests r...) [ 42%] -tests/core_test.py::test_long_pdb[1NXO] SKIPPED (not running tests r...) [ 42%] -tests/core_test.py::test_long_pdb[2IVY] SKIPPED (not running tests r...) [ 42%] -tests/core_test.py::test_long_pdb[2ZQE] SKIPPED (not running tests r...) [ 43%] -tests/core_test.py::test_long_pdb[2CGQ] SKIPPED (not running tests r...) [ 43%] -tests/core_test.py::test_long_pdb[1OX3] SKIPPED (not running tests r...) [ 43%] -tests/core_test.py::test_long_pdb[1TEN] SKIPPED (not running tests r...) [ 44%] -tests/core_test.py::test_long_pdb[3TSV] SKIPPED (not running tests r...) [ 44%] -tests/core_test.py::test_long_pdb[1L2P] SKIPPED (not running tests r...) [ 44%] -tests/core_test.py::test_long_pdb[2CJJ] SKIPPED (not running tests r...) [ 45%] -tests/core_test.py::test_long_pdb[2R6Q] SKIPPED (not running tests r...) [ 45%] -tests/core_test.py::test_long_pdb[1X91] SKIPPED (not running tests r...) [ 45%] -tests/core_test.py::test_long_pdb[3H0X] SKIPPED (not running tests r...) [ 46%] -tests/core_test.py::test_long_pdb[1HUF] SKIPPED (not running tests r...) [ 46%] -tests/core_test.py::test_long_pdb[3HRO] SKIPPED (not running tests r...) [ 46%] -tests/core_test.py::test_long_pdb[5V0O] SKIPPED (not running tests r...) [ 47%] -tests/core_test.py::test_long_pdb[3CQT] SKIPPED (not running tests r...) [ 47%] -tests/core_test.py::test_long_pdb[1OA4] SKIPPED (not running tests r...) [ 47%] -tests/core_test.py::test_long_pdb[2X4J] SKIPPED (not running tests r...) [ 48%] -tests/core_test.py::test_long_pdb[1RIS] SKIPPED (not running tests r...) [ 48%] -tests/core_test.py::test_long_pdb[1J2A] SKIPPED (not running tests r...) [ 48%] -tests/core_test.py::test_long_pdb[2BYG] SKIPPED (not running tests r...) [ 49%] -tests/core_test.py::test_long_pdb[4CFI] SKIPPED (not running tests r...) [ 49%] -tests/core_test.py::test_long_pdb[2H2C] SKIPPED (not running tests r...) [ 49%] -tests/core_test.py::test_long_pdb[3NGP] SKIPPED (not running tests r...) [ 50%] -tests/core_test.py::test_long_pdb[2TGI] SKIPPED (not running tests r...) [ 50%] -tests/core_test.py::test_long_pdb[2YXF] SKIPPED (not running tests r...) [ 50%] -tests/core_test.py::test_long_pdb[1P1L] SKIPPED (not running tests r...) [ 51%] -tests/core_test.py::test_long_pdb[3DVI] SKIPPED (not running tests r...) [ 51%] -tests/core_test.py::test_long_pdb[1KFN] SKIPPED (not running tests r...) [ 51%] -tests/core_test.py::test_long_pdb[1USM] SKIPPED (not running tests r...) [ 52%] -tests/core_test.py::test_long_pdb[1WOU] SKIPPED (not running tests r...) [ 52%] -tests/core_test.py::test_long_pdb[5EE2] SKIPPED (not running tests r...) [ 52%] -tests/core_test.py::test_long_pdb[4OSN] SKIPPED (not running tests r...) [ 53%] -tests/core_test.py::test_long_pdb[2CWR] SKIPPED (not running tests r...) [ 53%] -tests/core_test.py::test_long_pdb[1NOA] SKIPPED (not running tests r...) [ 53%] -tests/core_test.py::test_long_pdb[1TQG] SKIPPED (not running tests r...) [ 54%] -tests/core_test.py::test_long_pdb[4YKD] SKIPPED (not running tests r...) [ 54%] -tests/core_test.py::test_long_pdb[2NYC] SKIPPED (not running tests r...) [ 54%] -tests/core_test.py::test_long_pdb[2IGD] SKIPPED (not running tests r...) [ 55%] -tests/core_test.py::test_long_pdb[1NH9] SKIPPED (not running tests r...) [ 55%] -tests/core_test.py::test_long_pdb[1B0X] SKIPPED (not running tests r...) [ 55%] -tests/core_test.py::test_long_pdb[1PHT] SKIPPED (not running tests r...) [ 56%] -tests/core_test.py::test_long_pdb[3RVC] SKIPPED (not running tests r...) [ 56%] -tests/core_test.py::test_long_pdb[1TG0] SKIPPED (not running tests r...) [ 56%] -tests/core_test.py::test_long_pdb[2ESK] SKIPPED (not running tests r...) [ 57%] -tests/core_test.py::test_long_pdb[2JIC] SKIPPED (not running tests r...) [ 57%] -tests/core_test.py::test_long_pdb[1OPC] SKIPPED (not running tests r...) [ 57%] -tests/core_test.py::test_long_pdb[3JTE] SKIPPED (not running tests r...) [ 57%] -tests/core_test.py::test_long_pdb[1NKD] SKIPPED (not running tests r...) [ 58%] -tests/core_test.py::test_long_pdb[4LJ1] SKIPPED (not running tests r...) [ 58%] -tests/core_test.py::test_long_pdb[1HOE] SKIPPED (not running tests r...) [ 58%] -tests/core_test.py::test_long_pdb[2YGS] SKIPPED (not running tests r...) [ 59%] -tests/core_test.py::test_long_pdb[3RFI] SKIPPED (not running tests r...) [ 59%] -tests/core_test.py::test_long_pdb[3LS0] SKIPPED (not running tests r...) [ 59%] -tests/core_test.py::test_long_pdb[1I2T] SKIPPED (not running tests r...) [ 60%] -tests/core_test.py::test_long_pdb[2ERA] SKIPPED (not running tests r...) [ 60%] -tests/core_test.py::test_long_pdb[3B7H] SKIPPED (not running tests r...) [ 60%] -tests/core_test.py::test_long_pdb[4GMQ] SKIPPED (not running tests r...) [ 61%] -tests/core_test.py::test_long_pdb[2P5K] SKIPPED (not running tests r...) [ 61%] -tests/core_test.py::test_long_pdb[3ZSL] SKIPPED (not running tests r...) [ 61%] -tests/core_test.py::test_long_pdb[1TUD] SKIPPED (not running tests r...) [ 62%] -tests/core_test.py::test_long_pdb[1TVQ] SKIPPED (not running tests r...) [ 62%] -tests/core_test.py::test_long_pdb[2CMP] SKIPPED (not running tests r...) [ 62%] -tests/core_test.py::test_long_pdb[3LLB] SKIPPED (not running tests r...) [ 63%] -tests/core_test.py::test_long_pdb[2CKX] SKIPPED (not running tests r...) [ 63%] -tests/core_test.py::test_long_pdb[1DF4] SKIPPED (not running tests r...) [ 63%] -tests/core_test.py::test_long_pdb[1R7J] SKIPPED (not running tests r...) [ 64%] -tests/core_test.py::test_long_pdb[2PII] SKIPPED (not running tests r...) [ 64%] -tests/core_test.py::test_long_pdb[3RFF] SKIPPED (not running tests r...) [ 64%] -tests/core_test.py::test_long_pdb[3WFV] SKIPPED (not running tests r...) [ 65%] -tests/core_test.py::test_long_pdb[3FH2] SKIPPED (not running tests r...) [ 65%] -tests/core_test.py::test_long_pdb[1XAK] SKIPPED (not running tests r...) [ 65%] -tests/core_test.py::test_long_pdb[3I1G] SKIPPED (not running tests r...) [ 66%] -tests/core_test.py::test_long_pdb[1J27] SKIPPED (not running tests r...) [ 66%] -tests/core_test.py::test_long_pdb[1H75] SKIPPED (not running tests r...) [ 66%] -tests/core_test.py::test_long_pdb[3V1A] SKIPPED (not running tests r...) [ 67%] -tests/core_test.py::test_long_pdb[4ZMK] SKIPPED (not running tests r...) [ 67%] -tests/core_test.py::test_long_pdb[1PZC] SKIPPED (not running tests r...) [ 67%] -tests/core_test.py::test_long_pdb[2REY] SKIPPED (not running tests r...) [ 68%] -tests/core_test.py::test_broken_backbone[4MGP] +tests/core_test.py::test_long_pdb[2OP6] SKIPPED (not running tests r...) [ 25%] +tests/core_test.py::test_long_pdb[2PMR] SKIPPED (not running tests r...) [ 26%] +tests/core_test.py::test_long_pdb[4GMQ] SKIPPED (not running tests r...) [ 26%] +tests/core_test.py::test_long_pdb[1PDO] SKIPPED (not running tests r...) [ 26%] +tests/core_test.py::test_long_pdb[2FD4] SKIPPED (not running tests r...) [ 27%] +tests/core_test.py::test_long_pdb[1J2A] SKIPPED (not running tests r...) [ 27%] +tests/core_test.py::test_long_pdb[1ZX6] SKIPPED (not running tests r...) [ 27%] +tests/core_test.py::test_long_pdb[2IVY] SKIPPED (not running tests r...) [ 28%] +tests/core_test.py::test_long_pdb[4Q2Q] SKIPPED (not running tests r...) [ 28%] +tests/core_test.py::test_long_pdb[2IGD] SKIPPED (not running tests r...) [ 28%] +tests/core_test.py::test_long_pdb[1RJ1] SKIPPED (not running tests r...) [ 28%] +tests/core_test.py::test_long_pdb[1YQB] SKIPPED (not running tests r...) [ 29%] +tests/core_test.py::test_long_pdb[1IS5] SKIPPED (not running tests r...) [ 29%] +tests/core_test.py::test_long_pdb[2SGA] SKIPPED (not running tests r...) [ 29%] +tests/core_test.py::test_long_pdb[3NX6] SKIPPED (not running tests r...) [ 30%] +tests/core_test.py::test_long_pdb[3SO2] SKIPPED (not running tests r...) [ 30%] +tests/core_test.py::test_long_pdb[1ZVA] SKIPPED (not running tests r...) [ 30%] +tests/core_test.py::test_long_pdb[2PTV] SKIPPED (not running tests r...) [ 31%] +tests/core_test.py::test_long_pdb[4YPC] SKIPPED (not running tests r...) [ 31%] +tests/core_test.py::test_long_pdb[3WFV] SKIPPED (not running tests r...) [ 31%] +tests/core_test.py::test_long_pdb[2HC8] SKIPPED (not running tests r...) [ 32%] +tests/core_test.py::test_long_pdb[4ZMK] SKIPPED (not running tests r...) [ 32%] +tests/core_test.py::test_long_pdb[3RFI] SKIPPED (not running tests r...) [ 32%] +tests/core_test.py::test_long_pdb[1TQG] SKIPPED (not running tests r...) [ 33%] +tests/core_test.py::test_long_pdb[2R6Q] SKIPPED (not running tests r...) [ 33%] +tests/core_test.py::test_long_pdb[3ONJ] SKIPPED (not running tests r...) [ 33%] +tests/core_test.py::test_long_pdb[1NXO] SKIPPED (not running tests r...) [ 34%] +tests/core_test.py::test_long_pdb[3US6] SKIPPED (not running tests r...) [ 34%] +tests/core_test.py::test_long_pdb[4S11] SKIPPED (not running tests r...) [ 34%] +tests/core_test.py::test_long_pdb[3ZSL] SKIPPED (not running tests r...) [ 35%] +tests/core_test.py::test_long_pdb[3KT2] SKIPPED (not running tests r...) [ 35%] +tests/core_test.py::test_long_pdb[1OPS] SKIPPED (not running tests r...) [ 35%] +tests/core_test.py::test_long_pdb[2GZV] SKIPPED (not running tests r...) [ 36%] +tests/core_test.py::test_long_pdb[4CFI] SKIPPED (not running tests r...) [ 36%] +tests/core_test.py::test_long_pdb[4ZQA] SKIPPED (not running tests r...) [ 36%] +tests/core_test.py::test_long_pdb[1PHT] SKIPPED (not running tests r...) [ 37%] +tests/core_test.py::test_long_pdb[1AIL] SKIPPED (not running tests r...) [ 37%] +tests/core_test.py::test_long_pdb[3CP1] SKIPPED (not running tests r...) [ 37%] +tests/core_test.py::test_long_pdb[4GQM] SKIPPED (not running tests r...) [ 38%] +tests/core_test.py::test_long_pdb[1KFN] SKIPPED (not running tests r...) [ 38%] +tests/core_test.py::test_long_pdb[1OA4] SKIPPED (not running tests r...) [ 38%] +tests/core_test.py::test_long_pdb[3B7H] SKIPPED (not running tests r...) [ 39%] +tests/core_test.py::test_long_pdb[2OCH] SKIPPED (not running tests r...) [ 39%] +tests/core_test.py::test_long_pdb[4RWU] SKIPPED (not running tests r...) [ 39%] +tests/core_test.py::test_long_pdb[4NPN] SKIPPED (not running tests r...) [ 40%] +tests/core_test.py::test_long_pdb[3JTE] SKIPPED (not running tests r...) [ 40%] +tests/core_test.py::test_long_pdb[3RFF] SKIPPED (not running tests r...) [ 40%] +tests/core_test.py::test_long_pdb[4OSN] SKIPPED (not running tests r...) [ 41%] +tests/core_test.py::test_long_pdb[4YKD] SKIPPED (not running tests r...) [ 41%] +tests/core_test.py::test_long_pdb[4HS2] SKIPPED (not running tests r...) [ 41%] +tests/core_test.py::test_long_pdb[3IDW] SKIPPED (not running tests r...) [ 42%] +tests/core_test.py::test_long_pdb[4LJ1] SKIPPED (not running tests r...) [ 42%] +tests/core_test.py::test_long_pdb[3S0A] SKIPPED (not running tests r...) [ 42%] +tests/core_test.py::test_long_pdb[2ERA] SKIPPED (not running tests r...) [ 42%] +tests/core_test.py::test_long_pdb[1YIB] SKIPPED (not running tests r...) [ 43%] +tests/core_test.py::test_long_pdb[1JQ0] SKIPPED (not running tests r...) [ 43%] +tests/core_test.py::test_long_pdb[1B0X] SKIPPED (not running tests r...) [ 43%] +tests/core_test.py::test_long_pdb[3LMO] SKIPPED (not running tests r...) [ 44%] +tests/core_test.py::test_long_pdb[5V0O] SKIPPED (not running tests r...) [ 44%] +tests/core_test.py::test_long_pdb[2CGQ] SKIPPED (not running tests r...) [ 44%] +tests/core_test.py::test_long_pdb[3CSR] SKIPPED (not running tests r...) [ 45%] +tests/core_test.py::test_long_pdb[1J27] SKIPPED (not running tests r...) [ 45%] +tests/core_test.py::test_long_pdb[2PND] SKIPPED (not running tests r...) [ 45%] +tests/core_test.py::test_long_pdb[1NH9] SKIPPED (not running tests r...) [ 46%] +tests/core_test.py::test_long_pdb[1WOU] SKIPPED (not running tests r...) [ 46%] +tests/core_test.py::test_long_pdb[1RIS] SKIPPED (not running tests r...) [ 46%] +tests/core_test.py::test_long_pdb[3KZD] SKIPPED (not running tests r...) [ 47%] +tests/core_test.py::test_long_pdb[2P5K] SKIPPED (not running tests r...) [ 47%] +tests/core_test.py::test_long_pdb[2EBB] SKIPPED (not running tests r...) [ 47%] +tests/core_test.py::test_long_pdb[2FRG] SKIPPED (not running tests r...) [ 48%] +tests/core_test.py::test_long_pdb[2NSN] SKIPPED (not running tests r...) [ 48%] +tests/core_test.py::test_long_pdb[4TTW] SKIPPED (not running tests r...) [ 48%] +tests/core_test.py::test_long_pdb[2JCP] SKIPPED (not running tests r...) [ 49%] +tests/core_test.py::test_long_pdb[2FI9] SKIPPED (not running tests r...) [ 49%] +tests/core_test.py::test_long_pdb[3I1G] SKIPPED (not running tests r...) [ 49%] +tests/core_test.py::test_long_pdb[1TVQ] SKIPPED (not running tests r...) [ 50%] +tests/core_test.py::test_long_pdb[1P1L] SKIPPED (not running tests r...) [ 50%] +tests/core_test.py::test_long_pdb[3ISU] SKIPPED (not running tests r...) [ 50%] +tests/core_test.py::test_long_pdb[2X4J] SKIPPED (not running tests r...) [ 51%] +tests/core_test.py::test_long_pdb[1TIG] SKIPPED (not running tests r...) [ 51%] +tests/core_test.py::test_long_pdb[3NGP] SKIPPED (not running tests r...) [ 51%] +tests/core_test.py::test_long_pdb[3QC7] SKIPPED (not running tests r...) [ 52%] +tests/core_test.py::test_long_pdb[1OPC] SKIPPED (not running tests r...) [ 52%] +tests/core_test.py::test_long_pdb[3T8R] SKIPPED (not running tests r...) [ 52%] +tests/core_test.py::test_long_pdb[3LS0] SKIPPED (not running tests r...) [ 53%] +tests/core_test.py::test_long_pdb[3LLB] SKIPPED (not running tests r...) [ 53%] +tests/core_test.py::test_long_pdb[3T1S] SKIPPED (not running tests r...) [ 53%] +tests/core_test.py::test_long_pdb[2QBV] SKIPPED (not running tests r...) [ 54%] +tests/core_test.py::test_long_pdb[1TUD] SKIPPED (not running tests r...) [ 54%] +tests/core_test.py::test_long_pdb[3LAA] SKIPPED (not running tests r...) [ 54%] +tests/core_test.py::test_long_pdb[2SFA] SKIPPED (not running tests r...) [ 55%] +tests/core_test.py::test_long_pdb[2IBL] SKIPPED (not running tests r...) [ 55%] +tests/core_test.py::test_long_pdb[1X91] SKIPPED (not running tests r...) [ 55%] +tests/core_test.py::test_long_pdb[2JIC] SKIPPED (not running tests r...) [ 56%] +tests/core_test.py::test_long_pdb[1NKD] SKIPPED (not running tests r...) [ 56%] +tests/core_test.py::test_long_pdb[4CRH] SKIPPED (not running tests r...) [ 56%] +tests/core_test.py::test_long_pdb[2ERW] SKIPPED (not running tests r...) [ 57%] +tests/core_test.py::test_long_pdb[1I2T] SKIPPED (not running tests r...) [ 57%] +tests/core_test.py::test_long_pdb[1NOA] SKIPPED (not running tests r...) [ 57%] +tests/core_test.py::test_long_pdb[4POY] SKIPPED (not running tests r...) [ 57%] +tests/core_test.py::test_long_pdb[3CE7] SKIPPED (not running tests r...) [ 58%] +tests/core_test.py::test_long_pdb[1TEN] SKIPPED (not running tests r...) [ 58%] +tests/core_test.py::test_long_pdb[4IL7] SKIPPED (not running tests r...) [ 58%] +tests/core_test.py::test_long_pdb[1TGN] SKIPPED (not running tests r...) [ 59%] +tests/core_test.py::test_long_pdb[1HUF] SKIPPED (not running tests r...) [ 59%] +tests/core_test.py::test_long_pdb[2IWN] SKIPPED (not running tests r...) [ 59%] +tests/core_test.py::test_long_pdb[2NYC] SKIPPED (not running tests r...) [ 60%] +tests/core_test.py::test_long_pdb[1USM] SKIPPED (not running tests r...) [ 60%] +tests/core_test.py::test_long_pdb[1TG0] SKIPPED (not running tests r...) [ 60%] +tests/core_test.py::test_long_pdb[2YGS] SKIPPED (not running tests r...) [ 61%] +tests/core_test.py::test_long_pdb[4CVD] SKIPPED (not running tests r...) [ 61%] +tests/core_test.py::test_long_pdb[1E7G] SKIPPED (not running tests r...) [ 61%] +tests/core_test.py::test_long_pdb[4HTI] SKIPPED (not running tests r...) [ 62%] +tests/core_test.py::test_long_pdb[1DF4] SKIPPED (not running tests r...) [ 62%] +tests/core_test.py::test_long_pdb[2PII] SKIPPED (not running tests r...) [ 62%] +tests/core_test.py::test_long_pdb[1USE] SKIPPED (not running tests r...) [ 63%] +tests/core_test.py::test_long_pdb[2HP7] SKIPPED (not running tests r...) [ 63%] +tests/core_test.py::test_long_pdb[3DVI] SKIPPED (not running tests r...) [ 63%] +tests/core_test.py::test_long_pdb[3RJS] SKIPPED (not running tests r...) [ 64%] +tests/core_test.py::test_long_pdb[1X3O] SKIPPED (not running tests r...) [ 64%] +tests/core_test.py::test_long_pdb[2J6B] SKIPPED (not running tests r...) [ 64%] +tests/core_test.py::test_long_pdb[1PGX] SKIPPED (not running tests r...) [ 65%] +tests/core_test.py::test_long_pdb[1Z0P] SKIPPED (not running tests r...) [ 65%] +tests/core_test.py::test_long_pdb[2QVO] SKIPPED (not running tests r...) [ 65%] +tests/core_test.py::test_long_pdb[3ZHI] SKIPPED (not running tests r...) [ 66%] +tests/core_test.py::test_long_pdb[3QE1] SKIPPED (not running tests r...) [ 66%] +tests/core_test.py::test_long_pdb[5DV8] SKIPPED (not running tests r...) [ 66%] +tests/core_test.py::test_long_pdb[1H75] SKIPPED (not running tests r...) [ 67%] +tests/core_test.py::test_long_pdb[2ESK] SKIPPED (not running tests r...) [ 67%] +tests/core_test.py::test_long_pdb[3RVC] SKIPPED (not running tests r...) [ 67%] +tests/core_test.py::test_long_pdb[3H0X] SKIPPED (not running tests r...) [ 68%] +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_4MGP_0/4MGP.log +INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_broken_backbone_1EJG_0/1EJG.log INFO PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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 PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments. INFO PDB2PQR3.5.2:main.py:756 Loading topology files. -INFO PDB2PQR3.5.2:main.py:758 Loading molecule: 4MGP +INFO PDB2PQR3.5.2:main.py:758 Loading molecule: 1EJG XFAIL [ 68%] tests/core_test.py::test_broken_backbone[2V75] -------------------------------- 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_2V75_0/2V75.log INFO PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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). @@ -1232,50 +1275,50 @@ INFO PDB2PQR3.5.2:main.py:756 Loading topology files. INFO PDB2PQR3.5.2:main.py:758 Loading molecule: 2V75 XFAIL [ 68%] -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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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 PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments. INFO PDB2PQR3.5.2:main.py:756 Loading topology files. -INFO PDB2PQR3.5.2:main.py:758 Loading molecule: 1EJG +INFO PDB2PQR3.5.2:main.py:758 Loading molecule: 3U7T XFAIL [ 69%] -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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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 PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments. INFO PDB2PQR3.5.2:main.py:756 Loading topology files. -INFO PDB2PQR3.5.2:main.py:758 Loading molecule: 3U7T +INFO PDB2PQR3.5.2:main.py:758 Loading molecule: 4MGP XFAIL [ 69%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 69%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 69%] +tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 70%] +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_chain_whitespace_ff=AMBER.pqr] PASSED [ 70%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 70%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.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_ff=AMBER.pqr] PASSED [ 71%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 71%] -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 [ 72%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 72%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 72%] +tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 71%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.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/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 71%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.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/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 72%] +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/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 73%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 73%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 73%] -tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 74%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 74%] -tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 74%] +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/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 74%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 74%] +tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 74%] tests/io_test.py::test_read_qcd PASSED [ 75%] 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 [ 75%] @@ -1448,7 +1491,7 @@ tests/propka_test.py::test_propka_apo[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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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). @@ -1502,7 +1545,7 @@ 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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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). @@ -1546,7 +1589,7 @@ 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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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). @@ -1587,7 +1630,7 @@ 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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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). @@ -1627,7 +1670,7 @@ 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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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). @@ -1667,7 +1710,7 @@ 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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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). @@ -1707,7 +1750,7 @@ 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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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). @@ -1747,7 +1790,7 @@ 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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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). @@ -1767,7 +1810,7 @@ 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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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). @@ -1793,7 +1836,7 @@ 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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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). @@ -1824,7 +1867,7 @@ 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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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). @@ -1864,7 +1907,7 @@ 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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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). @@ -1904,7 +1947,7 @@ 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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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). @@ -1945,7 +1988,7 @@ 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 PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software. INFO PDB2PQR3.5.2:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.5.2: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). @@ -1986,7 +2029,7 @@ tests/test_version.py::test_version_exists PASSED [ 99%] tests/test_version.py::test_version PASSED [100%] -============ 88 passed, 215 skipped, 4 xfailed in 68.37s (0:01:08) ============= +============ 88 passed, 215 skipped, 4 xfailed in 208.31s (0:03:28) ============ create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -2004,115 +2047,115 @@ creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11 creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/run.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/inputgen.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/aa.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/debump.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/definitions.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/main.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/io.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/topology.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/psize.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/topology.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/peoe.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand -creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/__init__.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/peoe.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/mol2.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/mol2.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/cif.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/cif.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/__init__.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/debump.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/io.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/main.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/cells.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/pdb.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/structures.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/definitions.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/forcefield.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/aa.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/biomolecule.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/inputgen.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/config.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/residue.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/_version.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/psize.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/utilities.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/na.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/quatfit.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/_version.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/forcefield.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/aa.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/na.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__main__.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/psize.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/structures.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/cells.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/residue.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/config.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/biomolecule.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/definitions.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/pdb.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/main.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/_version.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/structures.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/optimize.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens +creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/structures.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/__init__.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/optimize.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/residue.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/forcefield.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/run.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__main__.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/cif.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/utilities.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/pdb.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/io.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/quatfit.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AMBER.names -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PARSE.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/CHARMM.names -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PEOEPB.names -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/SWANSON.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TOPOLOGY.xml -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AA.xml -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TYL06.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/NA.xml -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/SWANSON.names -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PATCHES.xml -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AMBER.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AMBER.names -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/CHARMM.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/HYDROGENS.xml -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PARSE.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PEOEPB.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TOPOLOGY.xml -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/NA.xml -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TYL06.names -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PEOEPB.names -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PEOEPB.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TYL06.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PARSE.names -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AMBER.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/CHARMM.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/quatfit.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr -creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens -creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/__init__.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/structures.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/optimize.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/structures.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/optimize.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens -copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/run.py to run.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/inputgen.py to inputgen.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/aa.py to aa.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/debump.py to debump.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/definitions.py to definitions.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/main.py to main.cpython-311.pyc +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PATCHES.xml -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat +creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/cif.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/io.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/structures.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/__init__.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/main.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/residue.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/biomolecule.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/_version.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/config.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/aa.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/utilities.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/psize.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/forcefield.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/quatfit.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/definitions.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/inputgen.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/cells.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/debump.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/na.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/pdb.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/debump.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/biomolecule.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/inputgen.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr +creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/topology.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/mol2.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/peoe.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand +creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/mol2.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/__init__.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ +copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/peoe.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/io.py to io.cpython-311.pyc byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/topology.py to topology.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/psize.py to psize.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/topology.py to topology.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/peoe.py to peoe.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__init__.py to __init__.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/mol2.py to mol2.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/cif.py to cif.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/_version.py to _version.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/forcefield.py to forcefield.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/aa.py to aa.cpython-311.pyc byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/na.py to na.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__main__.py to __main__.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/psize.py to psize.cpython-311.pyc byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/structures.py to structures.cpython-311.pyc byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/cells.py to cells.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/residue.py to residue.cpython-311.pyc byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/config.py to config.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/biomolecule.py to biomolecule.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__init__.py to __init__.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/utilities.py to utilities.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/definitions.py to definitions.cpython-311.pyc byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/pdb.py to pdb.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/io.py to io.cpython-311.pyc -byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/quatfit.py to quatfit.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/main.py to main.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/_version.py to _version.cpython-311.pyc byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/structures.py to structures.cpython-311.pyc byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/optimize.py to optimize.cpython-311.pyc byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__init__.py to __init__.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/residue.py to residue.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/forcefield.py to forcefield.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/run.py to run.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__init__.py to __init__.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__main__.py to __main__.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/cif.py to cif.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/utilities.py to utilities.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/quatfit.py to quatfit.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/debump.py to debump.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/biomolecule.py to biomolecule.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/inputgen.py to inputgen.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/topology.py to topology.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/mol2.py to mol2.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__init__.py to __init__.cpython-311.pyc +byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/peoe.py to peoe.cpython-311.pyc running install_egg_info running egg_info creating pdb2pqr.egg-info @@ -2173,12 +2216,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/11680/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/11680/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/49292 and its subdirectories -I: Current time: Mon Jul 8 06:55:54 -12 2024 -I: pbuilder-time-stamp: 1720464954 +I: removing directory /srv/workspace/pbuilder/11680 and its subdirectories +I: Current time: Wed Jun 7 02:38:33 +14 2023 +I: pbuilder-time-stamp: 1686055113