Diff of the two buildlogs: -- --- b1/build.log 2023-04-20 08:56:53.542091291 +0000 +++ b2/build.log 2023-04-20 09:24:35.104370998 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Apr 19 20:51:22 -12 2023 -I: pbuilder-time-stamp: 1681980682 +I: Current time: Thu May 23 05:19:58 +14 2024 +I: pbuilder-time-stamp: 1716391198 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ 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 @@ -29,135 +29,167 @@ 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/245127/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3532224/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 23 05:20 /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/3532224/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3532224/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='8298141274324a2f8efab6c28b531a79' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='245127' - PS1='# ' - PS2='> ' + INVOCATION_ID=58cb0921989e4b85855f5a52ae910668 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3532224 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.ByWQaoqZ/pbuilderrc_y6In --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.ByWQaoqZ/b1 --logfile b1/build.log pdb2pqr_3.5.2+dfsg-3.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.ByWQaoqZ/pbuilderrc_mdUy --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.ByWQaoqZ/b2 --logfile b2/build.log --extrapackages usrmerge pdb2pqr_3.5.2+dfsg-3.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos1-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Feb 12 08:05 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 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 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 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 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 02:43 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 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more - -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount - -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Feb 12 08:05 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 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/245127/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Feb 13 2023 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 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 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 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 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 2023 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 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 2023 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 2023 more + -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount + -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Feb 13 2023 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 May 23 05:20 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 2023 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 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/3532224/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -322,7 +354,7 @@ Get: 103 http://deb.debian.org/debian bookworm/main amd64 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx-rtd-theme all 1.2.0+dfsg-1 [27.7 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 python3-testfixtures all 7.0.4-1 [79.8 kB] -Fetched 65.3 MB in 1s (45.2 MB/s) +Fetched 65.3 MB in 2s (37.5 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 ... 19596 files and directories currently installed.) @@ -770,8 +802,19 @@ 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/3532224/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/3532224/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 @@ -862,7 +905,7 @@ 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 @@ -1000,228 +1043,228 @@ 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[1FAS] SKIPPED (not running tests ...) [ 0%] -tests/core_test.py::test_short_pdb[1AQO] 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[4UN3] SKIPPED (not running tests ...) [ 0%] -tests/core_test.py::test_short_pdb[1NAJ] SKIPPED (not running tests ...) [ 1%] -tests/core_test.py::test_short_pdb[4E8M] SKIPPED (not running tests ...) [ 1%] -tests/core_test.py::test_short_pdb[5D8V] 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[1K1I] SKIPPED (not running tests ...) [ 2%] -tests/core_test.py::test_basic_cif[1FAS] SKIPPED (not running tests ...) [ 2%] -tests/core_test.py::test_basic_cif[1AQO] SKIPPED (not running tests ...) [ 3%] +tests/core_test.py::test_short_pdb[5D8V] SKIPPED (not running tests ...) [ 0%] +tests/core_test.py::test_short_pdb[1FAS] SKIPPED (not running tests ...) 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[ 67%] -tests/core_test.py::test_long_pdb[1PGX] SKIPPED (not running tests r...) [ 67%] -tests/core_test.py::test_long_pdb[2GZV] SKIPPED (not running tests r...) [ 68%] -tests/core_test.py::test_broken_backbone[4MGP] +tests/core_test.py::test_long_pdb[2P5K] SKIPPED (not running tests r...) [ 67%] +tests/core_test.py::test_long_pdb[2X4J] SKIPPED (not running tests r...) [ 67%] +tests/core_test.py::test_long_pdb[2SFA] SKIPPED (not running tests r...) [ 68%] +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_4MGP_0/4MGP.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: 4MGP +INFO PDB2PQR3.5.2:main.py:758 Loading molecule: 3U7T XFAIL [ 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_1EJG_0/1EJG.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). @@ -1229,25 +1272,25 @@ INFO PDB2PQR3.5.2:main.py:756 Loading topology files. INFO PDB2PQR3.5.2:main.py:758 Loading molecule: 1EJG XFAIL [ 68%] -tests/core_test.py::test_broken_backbone[2V75] +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_2V75_0/2V75.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: 2V75 +INFO PDB2PQR3.5.2:main.py:758 Loading molecule: 4MGP XFAIL [ 69%] -tests/core_test.py::test_broken_backbone[3U7T] +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_3U7T_0/3U7T.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). 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: 2V75 XFAIL [ 69%] tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 69%] tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 70%] @@ -1271,8 +1314,8 @@ -------------------------------- 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%] @@ -1445,7 +1488,7 @@ 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). @@ -1499,7 +1542,7 @@ 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). @@ -1543,7 +1586,7 @@ 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). @@ -1584,7 +1627,7 @@ 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). @@ -1624,7 +1667,7 @@ 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). @@ -1664,7 +1707,7 @@ 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). @@ -1704,7 +1747,7 @@ 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). @@ -1744,7 +1787,7 @@ 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). @@ -1764,7 +1807,7 @@ 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). @@ -1790,7 +1833,7 @@ 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). @@ -1821,7 +1864,7 @@ 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). @@ -1861,7 +1904,7 @@ 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). @@ -1901,7 +1944,7 @@ 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). @@ -1942,7 +1985,7 @@ 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). @@ -1983,7 +2026,7 @@ tests/test_version.py::test_version_exists PASSED [ 99%] tests/test_version.py::test_version PASSED [100%] -============ 88 passed, 215 skipped, 4 xfailed in 214.84s (0:03:34) ============ +============ 88 passed, 215 skipped, 4 xfailed in 846.09s (0:14:06) ============ create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -2160,8 +2203,8 @@ dpkg-gencontrol: warning: package pdb2pqr-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'pdb2pqr-doc' in '../pdb2pqr-doc_3.5.2+dfsg-3_all.deb'. dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_3.5.2+dfsg-3_all.deb'. +dpkg-deb: building package 'pdb2pqr-doc' in '../pdb2pqr-doc_3.5.2+dfsg-3_all.deb'. dpkg-deb: building package 'python3-pdb2pqr' in '../python3-pdb2pqr_3.5.2+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../pdb2pqr_3.5.2+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../pdb2pqr_3.5.2+dfsg-3_amd64.changes @@ -2170,12 +2213,14 @@ 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/3532224/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3532224/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/245127 and its subdirectories -I: Current time: Wed Apr 19 20:56:53 -12 2023 -I: pbuilder-time-stamp: 1681981013 +I: removing directory /srv/workspace/pbuilder/3532224 and its subdirectories +I: Current time: Thu May 23 05:47:33 +14 2024 +I: pbuilder-time-stamp: 1716392853