https://launchpad.net/ubuntu/+source/pdb2pqr/3.6.1+dfsg-1/+build/26299803
RUN: /usr/share/launchpad-buildd/bin/builder-prep 
Kernel version: Linux lcy02-amd64-117 5.4.0-150-generic #167-Ubuntu SMP Mon May 15 17:35:05 UTC 2023 x86_64
Buildd toolchain package versions: launchpad-buildd_233~634~ubuntu20.04.1 python3-lpbuildd_233~634~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.
Syncing the system clock with the buildd NTP service...
12 Jun 23:14:15 ntpdate[1848]: adjust time server 10.131.248.1 offset 0.000127 sec
RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26299803 --image-type chroot /home/buildd/filecache-default/1fc1752c0976ad9eb0e621fd063fde252dab04e3
Creating target for build PACKAGEBUILD-26299803
RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26299803
Starting target for build PACKAGEBUILD-26299803
RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26299803 'deb http://ftpmaster.internal/ubuntu mantic main universe' 'deb http://ftpmaster.internal/ubuntu mantic-security main universe' 'deb http://ftpmaster.internal/ubuntu mantic-updates main universe' 'deb http://ftpmaster.internal/ubuntu mantic-proposed main universe'
Overriding sources.list in build-PACKAGEBUILD-26299803
RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26299803
Updating target for build PACKAGEBUILD-26299803
Get:1 http://ftpmaster.internal/ubuntu mantic InRelease [255 kB]
Get:2 http://ftpmaster.internal/ubuntu mantic-security InRelease [90.7 kB]
Get:3 http://ftpmaster.internal/ubuntu mantic-updates InRelease [90.7 kB]
Get:4 http://ftpmaster.internal/ubuntu mantic-proposed InRelease [118 kB]
Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 Packages [1396 kB]
Get:6 http://ftpmaster.internal/ubuntu mantic/main Translation-en [514 kB]
Get:7 http://ftpmaster.internal/ubuntu mantic/universe amd64 Packages [15.1 MB]
Get:8 http://ftpmaster.internal/ubuntu mantic/universe Translation-en [5926 kB]
Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 Packages [71.4 kB]
Get:10 http://ftpmaster.internal/ubuntu mantic-proposed/main Translation-en [26.3 kB]
Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 Packages [248 kB]
Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/universe Translation-en [112 kB]
Fetched 24.0 MB in 4s (6640 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following NEW packages will be installed:
  gcc-13-base libproc2-0
The following packages will be upgraded:
  adduser advancecomp apt base-files bash binutils binutils-common
  binutils-x86-64-linux-gnu bsdutils ca-certificates coreutils cpp cpp-12 dash
  debconf diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-12 gcc
  gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep hostname libacl1
  libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1
  libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6
  libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1
  libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0
  libdevmapper1.02.1 libdpkg-perl libext2fs2 libfakeroot libfdisk1
  libgcc-12-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgprofng0
  libgssapi-krb5-2 libisl23 libitm1 libk5crypto3 libkmod2 libkrb5-3
  libkrb5support0 liblsan0 liblzma5 libmount1 libmpfr6 libncurses6
  libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime
  libpam0g libpcre2-8-0 libperl5.36 libquadmath0 libreadline8 libseccomp2
  libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1
  libsqlite3-0 libss2 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared
  libsystemd0 libtinfo6 libtsan2 libubsan1 libudev1 libuuid1 libzstd1
  linux-libc-dev logsave lsb-base lto-disabled-list mount ncurses-base
  ncurses-bin openssl perl perl-base perl-modules-5.36 pkgbinarymangler procps
  readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tar
  tzdata usrmerge util-linux util-linux-extra xz-utils zlib1g
136 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 111 MB of archives.
After this operation, 433 kB disk space will be freed.
Get:1 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libcrypt-dev amd64 1:4.4.35-1 [112 kB]
Get:2 http://ftpmaster.internal/ubuntu mantic/main amd64 libc6-dev amd64 2.37-0ubuntu2 [2092 kB]
Get:3 http://ftpmaster.internal/ubuntu mantic/main amd64 libc-dev-bin amd64 2.37-0ubuntu2 [20.0 kB]
Get:4 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libcrypt1 amd64 1:4.4.35-1 [82.1 kB]
Get:5 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 linux-libc-dev amd64 6.3.0-7.7 [1544 kB]
Get:6 http://ftpmaster.internal/ubuntu mantic/main amd64 libc6 amd64 2.37-0ubuntu2 [3179 kB]
Get:7 http://ftpmaster.internal/ubuntu mantic/main amd64 libc-bin amd64 2.37-0ubuntu2 [669 kB]
Get:8 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-13-base amd64 13.1.0-2ubuntu2 [41.2 kB]
Get:9 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcc-s1 amd64 13.1.0-2ubuntu2 [62.4 kB]
Get:10 http://ftpmaster.internal/ubuntu mantic/main amd64 base-files amd64 12.3ubuntu3 [76.1 kB]
Get:11 http://ftpmaster.internal/ubuntu mantic/main amd64 bash amd64 5.2.15-2ubuntu1 [795 kB]
Get:12 http://ftpmaster.internal/ubuntu mantic/main amd64 bsdutils amd64 1:2.38.1-5ubuntu2 [91.5 kB]
Get:13 http://ftpmaster.internal/ubuntu mantic/main amd64 coreutils amd64 9.1-1ubuntu2 [1407 kB]
Get:14 http://ftpmaster.internal/ubuntu mantic/main amd64 liblzma5 amd64 5.4.1-0.2 [125 kB]
Get:15 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcrypt20 amd64 1.10.1-3ubuntu1 [529 kB]
Get:16 http://ftpmaster.internal/ubuntu mantic/main amd64 libstdc++6 amd64 13.1.0-2ubuntu2 [772 kB]
Get:17 http://ftpmaster.internal/ubuntu mantic/main amd64 libacl1 amd64 2.3.1-3 [16.4 kB]
Get:18 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libapparmor1 amd64 3.0.8-1ubuntu3 [46.3 kB]
Get:19 http://ftpmaster.internal/ubuntu mantic/main amd64 libaudit-common all 1:3.0.9-1 [5142 B]
Get:20 http://ftpmaster.internal/ubuntu mantic/main amd64 libcap-ng0 amd64 0.8.3-1build2 [15.3 kB]
Get:21 http://ftpmaster.internal/ubuntu mantic/main amd64 libaudit1 amd64 1:3.0.9-1 [46.0 kB]
Get:22 http://ftpmaster.internal/ubuntu mantic/main amd64 libblkid1 amd64 2.38.1-5ubuntu2 [111 kB]
Get:23 http://ftpmaster.internal/ubuntu mantic/main amd64 libcap2 amd64 1:2.66-4ubuntu1 [29.4 kB]
Get:24 http://ftpmaster.internal/ubuntu mantic/main amd64 libperl5.36 amd64 5.36.0-7ubuntu1 [4834 kB]
Get:25 http://ftpmaster.internal/ubuntu mantic/main amd64 perl amd64 5.36.0-7ubuntu1 [235 kB]
Get:26 http://ftpmaster.internal/ubuntu mantic/main amd64 perl-base amd64 5.36.0-7ubuntu1 [1784 kB]
Get:27 http://ftpmaster.internal/ubuntu mantic/main amd64 perl-modules-5.36 all 5.36.0-7ubuntu1 [2984 kB]
Get:28 http://ftpmaster.internal/ubuntu mantic/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [742 kB]
Get:29 http://ftpmaster.internal/ubuntu mantic/main amd64 zlib1g amd64 1:1.2.13.dfsg-1ubuntu4 [61.2 kB]
Get:30 http://ftpmaster.internal/ubuntu mantic/main amd64 debconf all 1.5.82 [125 kB]
Get:31 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libssl3 amd64 3.0.9-1ubuntu1 [1901 kB]
Get:32 http://ftpmaster.internal/ubuntu mantic/main amd64 libzstd1 amd64 1.5.4+dfsg2-5 [292 kB]
Get:33 http://ftpmaster.internal/ubuntu mantic/main amd64 libkmod2 amd64 30+20221128-1ubuntu1 [49.5 kB]
Get:34 http://ftpmaster.internal/ubuntu mantic/main amd64 libpcre2-8-0 amd64 10.42-1 [228 kB]
Get:35 http://ftpmaster.internal/ubuntu mantic/main amd64 libselinux1 amd64 3.4-1build4 [78.1 kB]
Get:36 http://ftpmaster.internal/ubuntu mantic/main amd64 libmount1 amd64 2.38.1-5ubuntu2 [121 kB]
Get:37 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam0g amd64 1.5.2-6ubuntu1 [65.9 kB]
Get:38 http://ftpmaster.internal/ubuntu mantic/main amd64 libseccomp2 amd64 2.5.4-1ubuntu3 [49.1 kB]
Get:39 http://ftpmaster.internal/ubuntu mantic/main amd64 systemd-sysv amd64 252.5-2ubuntu3 [11.5 kB]
Get:40 http://ftpmaster.internal/ubuntu mantic/main amd64 systemd amd64 252.5-2ubuntu3 [3002 kB]
Get:41 http://ftpmaster.internal/ubuntu mantic/main amd64 libsystemd-shared amd64 252.5-2ubuntu3 [1832 kB]
Get:42 http://ftpmaster.internal/ubuntu mantic/main amd64 libargon2-1 amd64 0~20190702+dfsg-3 [20.3 kB]
Get:43 http://ftpmaster.internal/ubuntu mantic/main amd64 libudev1 amd64 252.5-2ubuntu3 [150 kB]
Get:44 http://ftpmaster.internal/ubuntu mantic/main amd64 libdevmapper1.02.1 amd64 2:1.02.185-2ubuntu1 [139 kB]
Get:45 http://ftpmaster.internal/ubuntu mantic/main amd64 libuuid1 amd64 2.38.1-5ubuntu2 [32.7 kB]
Get:46 http://ftpmaster.internal/ubuntu mantic/main amd64 libcryptsetup12 amd64 2:2.6.1-4ubuntu1 [243 kB]
Get:47 http://ftpmaster.internal/ubuntu mantic/main amd64 libfdisk1 amd64 2.38.1-5ubuntu2 [144 kB]
Get:48 http://ftpmaster.internal/ubuntu mantic/main amd64 libp11-kit0 amd64 0.24.1-2ubuntu1 [248 kB]
Get:49 http://ftpmaster.internal/ubuntu mantic/main amd64 mount amd64 2.38.1-5ubuntu2 [114 kB]
Get:50 http://ftpmaster.internal/ubuntu mantic/main amd64 libsystemd0 amd64 252.5-2ubuntu3 [389 kB]
Get:51 http://ftpmaster.internal/ubuntu mantic/main amd64 libapt-pkg6.0 amd64 2.7.1 [930 kB]
Get:52 http://ftpmaster.internal/ubuntu mantic/main amd64 tar amd64 1.34+dfsg-1.2ubuntu1 [293 kB]
Get:53 http://ftpmaster.internal/ubuntu mantic/main amd64 dpkg amd64 1.21.22ubuntu1 [1393 kB]
Get:54 http://ftpmaster.internal/ubuntu mantic/main amd64 dash amd64 0.5.12-2ubuntu1 [88.2 kB]
Get:55 http://ftpmaster.internal/ubuntu mantic/main amd64 diffutils amd64 1:3.8-4 [176 kB]
Get:56 http://ftpmaster.internal/ubuntu mantic/main amd64 findutils amd64 4.9.0-4ubuntu1 [299 kB]
Get:57 http://ftpmaster.internal/ubuntu mantic/main amd64 grep amd64 3.8-5 [160 kB]
Get:58 http://ftpmaster.internal/ubuntu mantic/main amd64 hostname amd64 3.23+nmu1ubuntu1 [11.0 kB]
Get:59 http://ftpmaster.internal/ubuntu mantic/main amd64 ncurses-bin amd64 6.4-4 [185 kB]
Get:60 http://ftpmaster.internal/ubuntu mantic/main amd64 sed amd64 4.9-1 [193 kB]
Get:61 http://ftpmaster.internal/ubuntu mantic/main amd64 libsmartcols1 amd64 2.38.1-5ubuntu2 [59.5 kB]
Get:62 http://ftpmaster.internal/ubuntu mantic/main amd64 util-linux-extra amd64 2.38.1-5ubuntu2 [83.8 kB]
Get:63 http://ftpmaster.internal/ubuntu mantic/main amd64 util-linux amd64 2.38.1-5ubuntu2 [1075 kB]
Get:64 http://ftpmaster.internal/ubuntu mantic/main amd64 ncurses-base all 6.4-4 [23.3 kB]
Get:65 http://ftpmaster.internal/ubuntu mantic/main amd64 sysvinit-utils amd64 3.06-4ubuntu1 [33.0 kB]
Get:66 http://ftpmaster.internal/ubuntu mantic/main amd64 lsb-base all 11.6 [4606 B]
Get:67 http://ftpmaster.internal/ubuntu mantic/main amd64 adduser all 3.129ubuntu1 [59.0 kB]
Get:68 http://ftpmaster.internal/ubuntu mantic/main amd64 gpgv amd64 2.2.40-1.1ubuntu1 [140 kB]
Get:69 http://ftpmaster.internal/ubuntu mantic/main amd64 libgnutls30 amd64 3.7.9-2ubuntu1 [999 kB]
Get:70 http://ftpmaster.internal/ubuntu mantic/main amd64 apt amd64 2.7.1 [1359 kB]
Get:71 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-modules-bin amd64 1.5.2-6ubuntu1 [47.3 kB]
Get:72 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-modules amd64 1.5.2-6ubuntu1 [284 kB]
Get:73 http://ftpmaster.internal/ubuntu mantic/main amd64 logsave amd64 1.47.0-1ubuntu1 [14.2 kB]
Get:74 http://ftpmaster.internal/ubuntu mantic/main amd64 libext2fs2 amd64 1.47.0-1ubuntu1 [212 kB]
Get:75 http://ftpmaster.internal/ubuntu mantic/main amd64 e2fsprogs amd64 1.47.0-1ubuntu1 [598 kB]
Get:76 http://ftpmaster.internal/ubuntu mantic/main amd64 libattr1 amd64 1:2.5.1-4 [12.4 kB]
Get:77 http://ftpmaster.internal/ubuntu mantic/main amd64 libdebconfclient0 amd64 0.267ubuntu1 [7892 B]
Get:78 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-runtime all 1.5.2-6ubuntu1 [41.5 kB]
Get:79 http://ftpmaster.internal/ubuntu mantic/main amd64 libsemanage-common all 3.4-1build4 [9852 B]
Get:80 http://ftpmaster.internal/ubuntu mantic/main amd64 libsepol2 amd64 3.4-2.1 [301 kB]
Get:81 http://ftpmaster.internal/ubuntu mantic/main amd64 libsemanage2 amd64 3.4-1build4 [92.7 kB]
Get:82 http://ftpmaster.internal/ubuntu mantic/main amd64 libncurses6 amd64 6.4-4 [112 kB]
Get:83 http://ftpmaster.internal/ubuntu mantic/main amd64 libncursesw6 amd64 6.4-4 [147 kB]
Get:84 http://ftpmaster.internal/ubuntu mantic/main amd64 libtinfo6 amd64 6.4-4 [103 kB]
Get:85 http://ftpmaster.internal/ubuntu mantic/main amd64 usrmerge all 35ubuntu1 [58.2 kB]
Get:86 http://ftpmaster.internal/ubuntu mantic/main amd64 libcom-err2 amd64 1.47.0-1ubuntu1 [14.5 kB]
Get:87 http://ftpmaster.internal/ubuntu mantic/main amd64 libproc2-0 amd64 2:4.0.3-1ubuntu1 [55.9 kB]
Get:88 http://ftpmaster.internal/ubuntu mantic/main amd64 libss2 amd64 1.47.0-1ubuntu1 [16.8 kB]
Get:89 http://ftpmaster.internal/ubuntu mantic/main amd64 procps amd64 2:4.0.3-1ubuntu1 [609 kB]
Get:90 http://ftpmaster.internal/ubuntu mantic/main amd64 sensible-utils all 0.0.17+nmu1 [19.3 kB]
Get:91 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 openssl amd64 3.0.9-1ubuntu1 [1189 kB]
Get:92 http://ftpmaster.internal/ubuntu mantic/main amd64 ca-certificates all 20230311ubuntu1 [152 kB]
Get:93 http://ftpmaster.internal/ubuntu mantic/main amd64 libgssapi-krb5-2 amd64 1.20.1-2 [142 kB]
Get:94 http://ftpmaster.internal/ubuntu mantic/main amd64 libkrb5-3 amd64 1.20.1-2 [346 kB]
Get:95 http://ftpmaster.internal/ubuntu mantic/main amd64 libkrb5support0 amd64 1.20.1-2 [32.7 kB]
Get:96 http://ftpmaster.internal/ubuntu mantic/main amd64 libk5crypto3 amd64 1.20.1-2 [81.1 kB]
Get:97 http://ftpmaster.internal/ubuntu mantic/main amd64 readline-common all 8.2-1.3 [55.7 kB]
Get:98 http://ftpmaster.internal/ubuntu mantic/main amd64 libreadline8 amd64 8.2-1.3 [151 kB]
Get:99 http://ftpmaster.internal/ubuntu mantic/main amd64 libsqlite3-0 amd64 3.40.1-2 [660 kB]
Get:100 http://ftpmaster.internal/ubuntu mantic/main amd64 tzdata all 2023c-4exp1ubuntu1 [271 kB]
Get:101 http://ftpmaster.internal/ubuntu mantic/main amd64 xz-utils amd64 5.4.1-0.2 [270 kB]
Get:102 http://ftpmaster.internal/ubuntu mantic/main amd64 advancecomp amd64 2.5-1 [180 kB]
Get:103 http://ftpmaster.internal/ubuntu mantic/main amd64 libgprofng0 amd64 2.40-2ubuntu6 [897 kB]
Get:104 http://ftpmaster.internal/ubuntu mantic/main amd64 libctf0 amd64 2.40-2ubuntu6 [97.4 kB]
Get:105 http://ftpmaster.internal/ubuntu mantic/main amd64 libctf-nobfd0 amd64 2.40-2ubuntu6 [101 kB]
Get:106 http://ftpmaster.internal/ubuntu mantic/main amd64 binutils-x86-64-linux-gnu amd64 2.40-2ubuntu6 [2502 kB]
Get:107 http://ftpmaster.internal/ubuntu mantic/main amd64 libbinutils amd64 2.40-2ubuntu6 [633 kB]
Get:108 http://ftpmaster.internal/ubuntu mantic/main amd64 binutils amd64 2.40-2ubuntu6 [18.5 kB]
Get:109 http://ftpmaster.internal/ubuntu mantic/main amd64 binutils-common amd64 2.40-2ubuntu6 [239 kB]
Get:110 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libisl23 amd64 0.26-2 [755 kB]
Get:111 http://ftpmaster.internal/ubuntu mantic/main amd64 libmpfr6 amd64 4.2.0-1 [352 kB]
Get:112 http://ftpmaster.internal/ubuntu mantic/main amd64 g++-12 amd64 12.3.0-1ubuntu1 [12.1 MB]
Get:113 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-12 amd64 12.3.0-1ubuntu1 [21.6 MB]
Get:114 http://ftpmaster.internal/ubuntu mantic/main amd64 cpp-12 amd64 12.3.0-1ubuntu1 [10.7 MB]
Get:115 http://ftpmaster.internal/ubuntu mantic/main amd64 libubsan1 amd64 13.1.0-2ubuntu2 [1105 kB]
Get:116 http://ftpmaster.internal/ubuntu mantic/main amd64 libstdc++-12-dev amd64 12.3.0-1ubuntu1 [2178 kB]
Get:117 http://ftpmaster.internal/ubuntu mantic/main amd64 libgomp1 amd64 13.1.0-2ubuntu2 [142 kB]
Get:118 http://ftpmaster.internal/ubuntu mantic/main amd64 libitm1 amd64 13.1.0-2ubuntu2 [29.3 kB]
Get:119 http://ftpmaster.internal/ubuntu mantic/main amd64 libatomic1 amd64 13.1.0-2ubuntu2 [10.4 kB]
Get:120 http://ftpmaster.internal/ubuntu mantic/main amd64 libasan8 amd64 13.1.0-2ubuntu2 [2826 kB]
Get:121 http://ftpmaster.internal/ubuntu mantic/main amd64 liblsan0 amd64 13.1.0-2ubuntu2 [1203 kB]
Get:122 http://ftpmaster.internal/ubuntu mantic/main amd64 libquadmath0 amd64 13.1.0-2ubuntu2 [153 kB]
Get:123 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcc-12-dev amd64 12.3.0-1ubuntu1 [2577 kB]
Get:124 http://ftpmaster.internal/ubuntu mantic/main amd64 libtsan2 amd64 13.1.0-2ubuntu2 [2600 kB]
Get:125 http://ftpmaster.internal/ubuntu mantic/main amd64 libcc1-0 amd64 13.1.0-2ubuntu2 [48.1 kB]
Get:126 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-12-base amd64 12.3.0-1ubuntu1 [42.3 kB]
Get:127 http://ftpmaster.internal/ubuntu mantic/main amd64 g++ amd64 4:12.2.0-3ubuntu1 [1120 B]
Get:128 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc amd64 4:12.2.0-3ubuntu1 [5160 B]
Get:129 http://ftpmaster.internal/ubuntu mantic/main amd64 cpp amd64 4:12.2.0-3ubuntu1 [27.8 kB]
Get:130 http://ftpmaster.internal/ubuntu mantic/main amd64 dpkg-dev all 1.21.22ubuntu1 [1118 kB]
Get:131 http://ftpmaster.internal/ubuntu mantic/main amd64 libdpkg-perl all 1.21.22ubuntu1 [247 kB]
Get:132 http://ftpmaster.internal/ubuntu mantic/main amd64 lto-disabled-list all 41 [12.4 kB]
Get:133 http://ftpmaster.internal/ubuntu mantic/main amd64 libfakeroot amd64 1.31-1.2 [32.0 kB]
Get:134 http://ftpmaster.internal/ubuntu mantic/main amd64 fakeroot amd64 1.31-1.2 [60.1 kB]
Get:135 http://ftpmaster.internal/ubuntu mantic/main amd64 gpg amd64 2.2.40-1.1ubuntu1 [523 kB]
Get:136 http://ftpmaster.internal/ubuntu mantic/main amd64 gpgconf amd64 2.2.40-1.1ubuntu1 [96.3 kB]
Get:137 http://ftpmaster.internal/ubuntu mantic/main amd64 gpg-agent amd64 2.2.40-1.1ubuntu1 [216 kB]
Get:138 http://ftpmaster.internal/ubuntu mantic/main amd64 pkgbinarymangler all 153 [16.3 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 111 MB in 5s (20.6 MB/s)
(Reading database ... 13093 files and directories currently installed.)
Preparing to unpack .../libcrypt-dev_1%3a4.4.35-1_amd64.deb ...
Unpacking libcrypt-dev:amd64 (1:4.4.35-1) over (1:4.4.33-1) ...
Preparing to unpack .../libc6-dev_2.37-0ubuntu2_amd64.deb ...
Unpacking libc6-dev:amd64 (2.37-0ubuntu2) over (2.36-0ubuntu4) ...
Preparing to unpack .../libc-dev-bin_2.37-0ubuntu2_amd64.deb ...
Unpacking libc-dev-bin (2.37-0ubuntu2) over (2.36-0ubuntu4) ...
Preparing to unpack .../libcrypt1_1%3a4.4.35-1_amd64.deb ...
Unpacking libcrypt1:amd64 (1:4.4.35-1) over (1:4.4.33-1) ...
Setting up libcrypt1:amd64 (1:4.4.35-1) ...
(Reading database ... 13093 files and directories currently installed.)
Preparing to unpack .../linux-libc-dev_6.3.0-7.7_amd64.deb ...
Unpacking linux-libc-dev:amd64 (6.3.0-7.7) over (5.19.0-21.21) ...
Preparing to unpack .../libc6_2.37-0ubuntu2_amd64.deb ...
Unpacking libc6:amd64 (2.37-0ubuntu2) over (2.36-0ubuntu4) ...
Setting up libc6:amd64 (2.37-0ubuntu2) ...
(Reading database ... 13096 files and directories currently installed.)
Preparing to unpack .../libc-bin_2.37-0ubuntu2_amd64.deb ...
Unpacking libc-bin (2.37-0ubuntu2) over (2.36-0ubuntu4) ...
Setting up libc-bin (2.37-0ubuntu2) ...
Selecting previously unselected package gcc-13-base:amd64.
(Reading database ... 13096 files and directories currently installed.)
Preparing to unpack .../gcc-13-base_13.1.0-2ubuntu2_amd64.deb ...
Unpacking gcc-13-base:amd64 (13.1.0-2ubuntu2) ...
Setting up gcc-13-base:amd64 (13.1.0-2ubuntu2) ...
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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-26299803 amd64 mantic-proposed -c chroot:build-PACKAGEBUILD-26299803 --arch=amd64 --dist=mantic-proposed --nolog -A pdb2pqr_3.6.1+dfsg-1.dsc
Initiating build PACKAGEBUILD-26299803 with 4 jobs across 4 processor cores.
Kernel reported to sbuild: 5.4.0-150-generic #167-Ubuntu SMP Mon May 15 17:35:05 UTC 2023 x86_64
sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-117.buildd

+==============================================================================+
| pdb2pqr 3.6.1+dfsg-1 (amd64)                 Mon, 12 Jun 2023 23:15:02 +0000 |
+==============================================================================+

Package: pdb2pqr
Version: 3.6.1+dfsg-1
Source Version: 3.6.1+dfsg-1
Distribution: mantic-proposed
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: binary

I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26299803/chroot-autobuild' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/pdb2pqr-ihUOAn/resolver-ugeHuG' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Local sources
-------------

pdb2pqr_3.6.1+dfsg-1.dsc exists in .; copying to chroot
I: NOTICE: Log filtering will replace 'build/pdb2pqr-ihUOAn/pdb2pqr-3.6.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pdb2pqr-ihUOAn' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), dh-python, dh-sequence-sphinxdoc, help2man, python3-dev, python3-numpy, python3-pdbx, python3-pandas, python3-propka, python3-pytest, python3-setuptools, python3-sphinx-rtd-theme, python3-testfixtures, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), dh-python, dh-sequence-sphinxdoc, help2man, python3-dev, python3-numpy, python3-pdbx, python3-pandas, python3-propka, python3-pytest, python3-setuptools, python3-sphinx-rtd-theme, python3-testfixtures, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
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Reading package lists...
Reading package lists...

Install main build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit
  dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file
  fonts-font-awesome fonts-lato gettext gettext-base groff-base help2man
  intltool-debian libarchive-zip-perl libblas3 libdebhelper-perl libdw1
  libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl
  libgfortran5 libicu72 libjs-jquery libjs-sphinxdoc libjs-underscore
  libjson-perl liblapack3 liblocale-gettext-perl libmagic-mgc libmagic1
  libpipeline1 libpython3-dev libpython3-stdlib libpython3.11
  libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib
  libsub-override-perl libtool libuchardet0 libxml2 m4 man-db media-types
  po-debconf python-babel-localedata python3 python3-alabaster python3-attr
  python3-babel python3-certifi python3-chardet python3-dateutil python3-dev
  python3-distutils python3-docutils python3-idna python3-imagesize
  python3-iniconfig python3-jinja2 python3-lib2to3 python3-markupsafe
  python3-minimal python3-more-itertools python3-numpy python3-packaging
  python3-pandas python3-pandas-lib python3-pdbx python3-pkg-resources
  python3-pluggy python3-propka python3-py python3-pygments python3-pytest
  python3-requests python3-roman python3-setuptools python3-six
  python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme
  python3-testfixtures python3-tz python3-urllib3 python3.11 python3.11-dev
  python3.11-minimal sgml-base sphinx-common sphinx-rtd-theme-common xml-core
  zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build
  python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev
  groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
  www-browser libmail-box-perl python3-doc python3-tk python3-venv
  python-attr-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine
  texlive-lang-french texlive-latex-base texlive-latex-recommended
  python-jinja2-doc gfortran python-pandas-doc python3-statsmodels
  python-pdbx-doc python-propka-doc subversion python-pygments-doc
  ttf-bitstream-vera python3-cryptography python3-openssl python3-socks
  python-requests-doc python-setuptools-doc python3-stemmer dvipng
  fonts-freefont-otf imagemagick-6.q16 latexmk libjs-mathjax sphinx-doc
  tex-gyre texlive-fonts-recommended texlive-latex-extra texlive-plain-generic
  python-testfixtures-doc python3-brotli python3.11-venv python3.11-doc
  binfmt-support sgml-base-doc
Recommended packages:
  curl | wget | lynx libarchive-cpio-perl javascript-common libjson-xs-perl
  libltdl-dev libmail-sendmail-perl libpaper-utils python3-pil python3-scipy
  python3-matplotlib python3-bottleneck python3-numexpr python3-odf
  python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables
  python3-numba
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit
  dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file
  fonts-font-awesome fonts-lato gettext gettext-base groff-base help2man
  intltool-debian libarchive-zip-perl libblas3 libdebhelper-perl libdw1
  libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl
  libgfortran5 libicu72 libjs-jquery libjs-sphinxdoc libjs-underscore
  libjson-perl liblapack3 liblocale-gettext-perl libmagic-mgc libmagic1
  libpipeline1 libpython3-dev libpython3-stdlib libpython3.11
  libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib
  libsub-override-perl libtool libuchardet0 libxml2 m4 man-db media-types
  po-debconf python-babel-localedata python3 python3-alabaster python3-attr
  python3-babel python3-certifi python3-chardet python3-dateutil python3-dev
  python3-distutils python3-docutils python3-idna python3-imagesize
  python3-iniconfig python3-jinja2 python3-lib2to3 python3-markupsafe
  python3-minimal python3-more-itertools python3-numpy python3-packaging
  python3-pandas python3-pandas-lib python3-pdbx python3-pkg-resources
  python3-pluggy python3-propka python3-py python3-pygments python3-pytest
  python3-requests python3-roman python3-setuptools python3-six
  python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme
  python3-testfixtures python3-tz python3-urllib3 python3.11 python3.11-dev
  python3.11-minimal sbuild-build-depends-main-dummy sgml-base sphinx-common
  sphinx-rtd-theme-common xml-core zlib1g-dev
0 upgraded, 102 newly installed, 0 to remove and 0 not upgraded.
Need to get 66.2 MB of archives.
After this operation, 279 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [756 B]
Get:2 http://ftpmaster.internal/ubuntu mantic/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB]
Get:3 http://ftpmaster.internal/ubuntu mantic/main amd64 libpython3.11-minimal amd64 3.11.4-1 [839 kB]
Get:4 http://ftpmaster.internal/ubuntu mantic/main amd64 libexpat1 amd64 2.5.0-1 [84.2 kB]
Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 python3.11-minimal amd64 3.11.4-1 [2228 kB]
Get:6 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-minimal amd64 3.11.2-1 [24.6 kB]
Get:7 http://ftpmaster.internal/ubuntu mantic/main amd64 media-types all 10.0.0 [25.8 kB]
Get:8 http://ftpmaster.internal/ubuntu mantic/main amd64 libpython3.11-stdlib amd64 3.11.4-1 [1908 kB]
Get:9 http://ftpmaster.internal/ubuntu mantic/main amd64 python3.11 amd64 3.11.4-1 [572 kB]
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Get:11 http://ftpmaster.internal/ubuntu mantic/main amd64 python3 amd64 3.11.2-1 [22.9 kB]
Get:12 http://ftpmaster.internal/ubuntu mantic/main amd64 fonts-lato all 2.0-2.1 [2696 kB]
Get:13 http://ftpmaster.internal/ubuntu mantic/main amd64 sgml-base all 1.31 [11.4 kB]
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Get:15 http://ftpmaster.internal/ubuntu mantic/main amd64 libicu72 amd64 72.1-3ubuntu2 [10.8 MB]
Get:16 http://ftpmaster.internal/ubuntu mantic/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [764 kB]
Get:17 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 python3-pkg-resources all 67.8.0-1 [161 kB]
Get:18 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-pygments all 2.15.1+dfsg-1 [820 kB]
Get:19 http://ftpmaster.internal/ubuntu mantic/main amd64 bsdextrautils amd64 2.38.1-5ubuntu2 [71.0 kB]
Get:20 http://ftpmaster.internal/ubuntu mantic/main amd64 libmagic-mgc amd64 1:5.44-3 [293 kB]
Get:21 http://ftpmaster.internal/ubuntu mantic/main amd64 libmagic1 amd64 1:5.44-3 [85.6 kB]
Get:22 http://ftpmaster.internal/ubuntu mantic/main amd64 file amd64 1:5.44-3 [21.8 kB]
Get:23 http://ftpmaster.internal/ubuntu mantic/main amd64 gettext-base amd64 0.21-12 [38.0 kB]
Get:24 http://ftpmaster.internal/ubuntu mantic/main amd64 libuchardet0 amd64 0.0.7-1build2 [76.9 kB]
Get:25 http://ftpmaster.internal/ubuntu mantic/main amd64 groff-base amd64 1.22.4-10 [937 kB]
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Get:28 http://ftpmaster.internal/ubuntu mantic/main amd64 m4 amd64 1.4.19-3 [243 kB]
Get:29 http://ftpmaster.internal/ubuntu mantic/main amd64 autoconf all 2.71-3 [339 kB]
Get:30 http://ftpmaster.internal/ubuntu mantic/main amd64 autotools-dev all 20220109.1 [44.9 kB]
Get:31 http://ftpmaster.internal/ubuntu mantic/main amd64 automake all 1:1.16.5-1.3 [558 kB]
Get:32 http://ftpmaster.internal/ubuntu mantic/main amd64 autopoint all 0.21-12 [422 kB]
Get:33 http://ftpmaster.internal/ubuntu mantic/main amd64 libdebhelper-perl all 13.11.4ubuntu3 [66.1 kB]
Get:34 http://ftpmaster.internal/ubuntu mantic/main amd64 libtool all 2.4.7-5 [166 kB]
Get:35 http://ftpmaster.internal/ubuntu mantic/main amd64 dh-autoreconf all 20 [16.1 kB]
Get:36 http://ftpmaster.internal/ubuntu mantic/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB]
Get:37 http://ftpmaster.internal/ubuntu mantic/main amd64 libsub-override-perl all 0.09-4 [8706 B]
Get:38 http://ftpmaster.internal/ubuntu mantic/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB]
Get:39 http://ftpmaster.internal/ubuntu mantic/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B]
Get:40 http://ftpmaster.internal/ubuntu mantic/main amd64 libdw1 amd64 0.188-2.1 [251 kB]
Get:41 http://ftpmaster.internal/ubuntu mantic/main amd64 debugedit amd64 1:5.0-5 [46.1 kB]
Get:42 http://ftpmaster.internal/ubuntu mantic/main amd64 dwz amd64 0.15-1 [112 kB]
Get:43 http://ftpmaster.internal/ubuntu mantic/main amd64 gettext amd64 0.21-12 [866 kB]
Get:44 http://ftpmaster.internal/ubuntu mantic/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB]
Get:45 http://ftpmaster.internal/ubuntu mantic/main amd64 po-debconf all 1.0.21+nmu1 [233 kB]
Get:46 http://ftpmaster.internal/ubuntu mantic/main amd64 debhelper all 13.11.4ubuntu3 [925 kB]
Get:47 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 python3-lib2to3 all 3.11.4-1 [79.0 kB]
Get:48 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 python3-distutils all 3.11.4-1 [131 kB]
Get:49 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 dh-python all 6.20230603 [107 kB]
Get:50 http://ftpmaster.internal/ubuntu mantic/main amd64 xml-core all 0.18+nmu1 [21.6 kB]
Get:51 http://ftpmaster.internal/ubuntu mantic/main amd64 docutils-common all 0.19+dfsg-6 [129 kB]
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Get:59 http://ftpmaster.internal/ubuntu mantic/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB]
Get:60 http://ftpmaster.internal/ubuntu mantic/main amd64 libjson-perl all 4.10000-1 [81.9 kB]
Get:61 http://ftpmaster.internal/ubuntu mantic/main amd64 liblapack3 amd64 3.11.0-2 [2659 kB]
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Get:63 http://ftpmaster.internal/ubuntu mantic/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1ubuntu4 [895 kB]
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Get:68 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 python3-tz all 2023.3-2 [31.9 kB]
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Get:70 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-certifi all 2022.9.24-1 [155 kB]
Get:71 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-chardet all 5.1.0+dfsg-2 [119 kB]
Get:72 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-six all 1.16.0-4 [12.4 kB]
Get:73 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-dateutil all 2.8.2-2 [79.2 kB]
Get:74 http://ftpmaster.internal/ubuntu mantic/main amd64 python3.11-dev amd64 3.11.4-1 [618 kB]
Get:75 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-dev amd64 3.11.2-1 [26.8 kB]
Get:76 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-roman all 3.3-3 [9632 B]
Get:77 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-docutils all 0.19+dfsg-6 [386 kB]
Get:78 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-idna all 3.3-1 [49.3 kB]
Get:79 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-imagesize all 1.4.1-1 [6844 B]
Get:80 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B]
Get:81 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-markupsafe amd64 2.1.2-1build1 [12.4 kB]
Get:82 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-jinja2 all 3.1.2-1 [107 kB]
Get:83 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-more-itertools all 8.10.0-2 [47.9 kB]
Get:84 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-numpy amd64 1:1.24.2-1 [5573 kB]
Get:85 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 python3-packaging all 23.1-1 [38.1 kB]
Get:86 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-pandas-lib amd64 1.5.3+dfsg-2 [3756 kB]
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Get:88 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-pdbx all 2.0.1-2 [16.5 kB]
Get:89 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-pluggy all 1.0.0+repack-1 [15.1 kB]
Get:90 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-propka all 3.5.0-1 [67.4 kB]
Get:91 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-py all 1.11.0-1 [73.2 kB]
Get:92 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-pytest all 7.2.1-2 [237 kB]
Get:93 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-urllib3 all 1.26.12-1 [99.7 kB]
Get:94 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-requests all 2.28.1+dfsg-1ubuntu2 [50.7 kB]
Get:95 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 python3-setuptools all 67.8.0-1 [392 kB]
Get:96 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 python3-snowballstemmer all 2.2.0-4 [59.7 kB]
Get:97 http://ftpmaster.internal/ubuntu mantic/main amd64 sphinx-common all 5.3.0-4 [691 kB]
Get:98 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-alabaster all 0.7.12-1 [17.8 kB]
Get:99 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-sphinx all 5.3.0-4 [556 kB]
Get:100 http://ftpmaster.internal/ubuntu mantic/main amd64 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [991 kB]
Get:101 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-sphinx-rtd-theme all 1.2.0+dfsg-1 [23.1 kB]
Get:102 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-testfixtures all 7.0.4-1 [69.0 kB]
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Not building database; man-db/auto-update is not 'true'.
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Setting up python3-pygments (2.15.1+dfsg-1) ...
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Processing triggers for libc-bin (2.37-0ubuntu2) ...
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Setting up docutils-common (0.19+dfsg-6) ...
Processing triggers for sgml-base (1.31) ...
Setting up python3-docutils (0.19+dfsg-6) ...
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Setting up python3-sphinx-rtd-theme (1.2.0+dfsg-1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (amd64 included in all)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 5.4.0-150-generic #167-Ubuntu SMP Mon May 15 17:35:05 UTC 2023 amd64 (x86_64)
Toolchain package versions: binutils_2.40-2ubuntu6 dpkg-dev_1.21.22ubuntu1 g++-12_12.3.0-1ubuntu1 gcc-12_12.3.0-1ubuntu1 libc6-dev_2.37-0ubuntu2 libstdc++-12-dev_12.3.0-1ubuntu1 libstdc++6_13.1.0-2ubuntu2 linux-libc-dev_6.3.0-7.7
Package versions: adduser_3.129ubuntu1 advancecomp_2.5-1 apt_2.7.1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-12 autotools-dev_20220109.1 base-files_12.3ubuntu3 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 binutils_2.40-2ubuntu6 binutils-common_2.40-2ubuntu6 binutils-x86-64-linux-gnu_2.40-2ubuntu6 bsdextrautils_2.38.1-5ubuntu2 bsdutils_1:2.38.1-5ubuntu2 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 coreutils_9.1-1ubuntu2 cpp_4:12.2.0-3ubuntu1 cpp-12_12.3.0-1ubuntu1 dash_0.5.12-2ubuntu1 debconf_1.5.82 debhelper_13.11.4ubuntu3 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-python_6.20230603 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 docutils-common_0.19+dfsg-6 dpkg_1.21.22ubuntu1 dpkg-dev_1.21.22ubuntu1 dwz_0.15-1 e2fsprogs_1.47.0-1ubuntu1 fakeroot_1.31-1.2 file_1:5.44-3 findutils_4.9.0-4ubuntu1 fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1 fonts-lato_2.0-2.1 g++_4:12.2.0-3ubuntu1 g++-12_12.3.0-1ubuntu1 gcc_4:12.2.0-3ubuntu1 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libpython3.11-minimal_3.11.4-1 libpython3.11-stdlib_3.11.4-1 libquadmath0_13.1.0-2ubuntu2 libreadline8_8.2-1.3 libseccomp2_2.5.4-1ubuntu3 libselinux1_3.4-1build4 libsemanage-common_3.4-1build4 libsemanage2_3.4-1build4 libsepol2_3.4-2.1 libsmartcols1_2.38.1-5ubuntu2 libsqlite3-0_3.40.1-2 libss2_1.47.0-1ubuntu1 libssl3_3.0.9-1ubuntu1 libstdc++-12-dev_12.3.0-1ubuntu1 libstdc++6_13.1.0-2ubuntu2 libsub-override-perl_0.09-4 libsystemd-shared_252.5-2ubuntu3 libsystemd0_252.5-2ubuntu3 libtasn1-6_4.19.0-2 libtinfo6_6.4-4 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libtsan2_13.1.0-2ubuntu2 libubsan1_13.1.0-2ubuntu2 libuchardet0_0.0.7-1build2 libudev1_252.5-2ubuntu3 libunistring2_1.0-2 libuuid1_2.38.1-5ubuntu2 libxml2_2.9.14+dfsg-1.2 libxxhash0_0.8.1-1 libzstd1_1.5.4+dfsg2-5 linux-libc-dev_6.3.0-7.7 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.47.0-1ubuntu1 lsb-base_11.6 lto-disabled-list_41 m4_1.4.19-3 make_4.3-4.1build1 man-db_2.11.2-2 mawk_1.3.4.20200120-3.1 media-types_10.0.0 mount_2.38.1-5ubuntu2 ncurses-base_6.4-4 ncurses-bin_6.4-4 openssl_3.0.9-1ubuntu1 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-7ubuntu1 perl-base_5.36.0-7ubuntu1 perl-modules-5.36_5.36.0-7ubuntu1 pinentry-curses_1.2.1-1ubuntu1 pkgbinarymangler_153 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.3-1ubuntu1 python-babel-localedata_2.10.3-1 python3_3.11.2-1 python3-alabaster_0.7.12-1 python3-attr_22.2.0-1 python3-babel_2.10.3-1 python3-certifi_2022.9.24-1 python3-chardet_5.1.0+dfsg-2 python3-dateutil_2.8.2-2 python3-dev_3.11.2-1 python3-distutils_3.11.4-1 python3-docutils_0.19+dfsg-6 python3-idna_3.3-1 python3-imagesize_1.4.1-1 python3-iniconfig_1.1.1-2 python3-jinja2_3.1.2-1 python3-lib2to3_3.11.4-1 python3-markupsafe_2.1.2-1build1 python3-minimal_3.11.2-1 python3-more-itertools_8.10.0-2 python3-numpy_1:1.24.2-1 python3-packaging_23.1-1 python3-pandas_1.5.3+dfsg-2 python3-pandas-lib_1.5.3+dfsg-2 python3-pdbx_2.0.1-2 python3-pkg-resources_67.8.0-1 python3-pluggy_1.0.0+repack-1 python3-propka_3.5.0-1 python3-py_1.11.0-1 python3-pygments_2.15.1+dfsg-1 python3-pytest_7.2.1-2 python3-requests_2.28.1+dfsg-1ubuntu2 python3-roman_3.3-3 python3-setuptools_67.8.0-1 python3-six_1.16.0-4 python3-snowballstemmer_2.2.0-4 python3-sphinx_5.3.0-4 python3-sphinx-rtd-theme_1.2.0+dfsg-1 python3-testfixtures_7.0.4-1 python3-tz_2023.3-2 python3-urllib3_1.26.12-1 python3.11_3.11.4-1 python3.11-dev_3.11.4-1 python3.11-minimal_3.11.4-1 readline-common_8.2-1.3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.17+nmu1 sgml-base_1.31 sphinx-common_5.3.0-4 sphinx-rtd-theme-common_1.2.0+dfsg-1 systemd_252.5-2ubuntu3 systemd-sysv_252.5-2ubuntu3 sysvinit-utils_3.06-4ubuntu1 tar_1.34+dfsg-1.2ubuntu1 tzdata_2023c-4exp1ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_35ubuntu1 util-linux_2.38.1-5ubuntu2 util-linux-extra_2.38.1-5ubuntu2 xml-core_0.18+nmu1 xz-utils_5.4.1-0.2 zlib1g_1:1.2.13.dfsg-1ubuntu4 zlib1g-dev_1:1.2.13.dfsg-1ubuntu4

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 3.0 (quilt)
Source: pdb2pqr
Binary: pdb2pqr, pdb2pqr-doc, python3-pdb2pqr
Architecture: all
Version: 3.6.1+dfsg-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>, Manuel Prinz <manuel@debian.org>, Andreas Tille <tille@debian.org>
Homepage: https://www.poissonboltzmann.org
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/pdb2pqr
Vcs-Git: https://salsa.debian.org/med-team/pdb2pqr.git
Testsuite: autopkgtest
Testsuite-Triggers: python3-pandas, python3-pytest, python3-testfixtures
Build-Depends: debhelper-compat (= 13), dh-python, dh-sequence-sphinxdoc, help2man, python3-dev, python3-numpy, python3-pdbx, python3-pandas <!nocheck>, python3-propka <!nocheck>, python3-pytest <!nocheck>, python3-setuptools, python3-sphinx-rtd-theme, python3-testfixtures <!nocheck>
Package-List:
 pdb2pqr deb science optional arch=all
 pdb2pqr-doc deb doc optional arch=all
 python3-pdb2pqr deb python optional arch=all
Checksums-Sha1:
 1abfbc3018f13383334a6f4fad2b5f9261ef07d6 7570280 pdb2pqr_3.6.1+dfsg.orig.tar.xz
 2f47c850fcb1389cd2263ad77e15c1a249ff3dc2 9876 pdb2pqr_3.6.1+dfsg-1.debian.tar.xz
Checksums-Sha256:
 7c8587b124002a323611b7004565545731da9ea3350b89d1a7c67d5126863f98 7570280 pdb2pqr_3.6.1+dfsg.orig.tar.xz
 5d67facc48e503533313c3dc87f996da5858b631be7dfaf4e06bd61c2b74f7e3 9876 pdb2pqr_3.6.1+dfsg-1.debian.tar.xz
Files:
 512f5e6a68fbf1694326b4ef98d1dd76 7570280 pdb2pqr_3.6.1+dfsg.orig.tar.xz
 e648e2b04d779679b845ea20b2235b47 9876 pdb2pqr_3.6.1+dfsg-1.debian.tar.xz

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gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC
gpgv:                using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found
dpkg-source: info: extracting pdb2pqr in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking pdb2pqr_3.6.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking pdb2pqr_3.6.1+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying skip-network-tests.patch
dpkg-source: info: applying unversioned_docutils.patch

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-26299803
SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26299803
SCHROOT_COMMAND=env
SCHROOT_GID=2501
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=build-PACKAGEBUILD-26299803
SCHROOT_UID=2001
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=unknown
USER=buildd
V=1

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon <buildd@lcy02-amd64-117.buildd> -b -rfakeroot
dpkg-buildpackage: info: source package pdb2pqr
dpkg-buildpackage: info: source version 3.6.1+dfsg-1
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean --buildsystem pybuild --with python3
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
I: pybuild base:275: python3.11 setup.py clean 
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build' (and everything under it)
'build/bdist.linux-x86_64' does not exist -- can't clean it
'build/scripts-3.11' does not exist -- can't clean it
rm -rf pdb2pqr.egg-info
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary
dh binary --buildsystem pybuild --with python3
   dh_update_autotools_config -O--buildsystem=pybuild
   dh_autoreconf -O--buildsystem=pybuild
   dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:275: python3.11 setup.py config 
running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
I: pybuild base:275: /usr/bin/python3 setup.py build 
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/run.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/psize.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/residue.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/biomolecule.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/quatfit.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/config.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/inputgen.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/__main__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/definitions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/pdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/debump.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/main.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/forcefield.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/structures.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/topology.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/cif.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/utilities.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/na.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/aa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/_version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/cells.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/io.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens
copying pdb2pqr/hydrogens/structures.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens
copying pdb2pqr/hydrogens/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens
copying pdb2pqr/hydrogens/optimize.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/ligand
copying pdb2pqr/ligand/peoe.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/ligand
copying pdb2pqr/ligand/mol2.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/ligand
copying pdb2pqr/ligand/topology.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/ligand
copying pdb2pqr/ligand/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/ligand
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/TOPOLOGY.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/HYDROGENS.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/PATCHES.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/NA.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/AA.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/CHARMM.DAT -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/AMBER.DAT -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/PEOEPB.DAT -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/PARSE.DAT -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/SWANSON.DAT -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/TYL06.DAT -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/PARSE.names -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/AMBER.names -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/PEOEPB.names -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/SWANSON.names -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/CHARMM.names -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/TYL06.names -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat
PYTHONPATH=. python3 -m sphinx -N -bhtml docs/source build/html
Running Sphinx v5.3.0
making output directory... done
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 <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7fb14058ca10>: 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
updating environment: [new config] 39 added, 0 changed, 0 removed
reading sources... [  2%] api/aa
reading sources... [  5%] api/biomolecule
reading sources... [  7%] api/cells
reading sources... [ 10%] api/cif
reading sources... [ 12%] api/config
reading sources... [ 15%] api/debump
reading sources... [ 17%] api/definitions
reading sources... [ 20%] api/forcefield
reading sources... [ 23%] api/hydrogens
reading sources... [ 25%] api/index
reading sources... [ 28%] api/inputgen
reading sources... [ 30%] api/io
reading sources... [ 33%] api/ligand
reading sources... [ 35%] api/main
reading sources... [ 38%] api/na
reading sources... [ 41%] api/pdb
reading sources... [ 43%] api/psize
reading sources... [ 46%] api/quatfit
reading sources... [ 48%] api/residue
reading sources... [ 51%] api/run
reading sources... [ 53%] api/structures
reading sources... [ 56%] api/topology
reading sources... [ 58%] api/utilities
reading sources... [ 61%] extending
reading sources... [ 64%] formats/dat
reading sources... [ 66%] formats/index
reading sources... [ 69%] formats/mol2
reading sources... [ 71%] formats/pdb
reading sources... [ 74%] formats/pqr
reading sources... [ 76%] formats/xml-names
reading sources... [ 79%] getting
reading sources... [ 82%] help
reading sources... [ 84%] index
reading sources... [ 87%] releases
reading sources... [ 89%] supporting
reading sources... [ 92%] using/algorithms
reading sources... [ 94%] using/examples
reading sources... [ 97%] using/index
reading sources... [100%] using/other-software

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  2%] api/aa
writing output... [  5%] api/biomolecule
writing output... [  7%] api/cells
writing output... [ 10%] api/cif
writing output... [ 12%] api/config
writing output... [ 15%] api/debump
writing output... [ 17%] api/definitions
writing output... [ 20%] api/forcefield
writing output... [ 23%] api/hydrogens
writing output... [ 25%] api/index
writing output... [ 28%] api/inputgen
writing output... [ 30%] api/io
writing output... [ 33%] api/ligand
writing output... [ 35%] api/main
writing output... [ 38%] api/na
writing output... [ 41%] api/pdb
writing output... [ 43%] api/psize
writing output... [ 46%] api/quatfit
writing output... [ 48%] api/residue
writing output... [ 51%] api/run
writing output... [ 53%] api/structures
writing output... [ 56%] api/topology
writing output... [ 58%] api/utilities
writing output... [ 61%] extending
writing output... [ 64%] formats/dat
writing output... [ 66%] formats/index
writing output... [ 69%] formats/mol2
writing output... [ 71%] formats/pdb
writing output... [ 74%] formats/pqr
writing output... [ 76%] formats/xml-names
writing output... [ 79%] getting
writing output... [ 82%] help
writing output... [ 84%] index
writing output... [ 87%] releases
writing output... [ 89%] supporting
writing output... [ 92%] using/algorithms
writing output... [ 94%] using/examples
writing output... [ 97%] using/index
writing output... [100%] using/other-software

generating indices... genindex py-modindex done
highlighting module code... [  4%] pdb2pqr.aa
highlighting module code... [  8%] pdb2pqr.biomolecule
highlighting module code... [ 12%] pdb2pqr.cells
highlighting module code... [ 16%] pdb2pqr.cif
highlighting module code... [ 20%] pdb2pqr.debump
highlighting module code... [ 24%] pdb2pqr.definitions
highlighting module code... [ 28%] pdb2pqr.forcefield
highlighting module code... [ 32%] pdb2pqr.hydrogens
highlighting module code... [ 36%] pdb2pqr.hydrogens.optimize
highlighting module code... [ 40%] pdb2pqr.hydrogens.structures
highlighting module code... [ 44%] pdb2pqr.inputgen
highlighting module code... [ 48%] pdb2pqr.io
highlighting module code... [ 52%] pdb2pqr.ligand.mol2
highlighting module code... [ 56%] pdb2pqr.ligand.peoe
highlighting module code... [ 60%] pdb2pqr.ligand.topology
highlighting module code... [ 64%] pdb2pqr.main
highlighting module code... [ 68%] pdb2pqr.na
highlighting module code... [ 72%] pdb2pqr.pdb
highlighting module code... [ 76%] pdb2pqr.psize
highlighting module code... [ 80%] pdb2pqr.quatfit
highlighting module code... [ 84%] pdb2pqr.residue
highlighting module code... [ 88%] pdb2pqr.run
highlighting module code... [ 92%] pdb2pqr.structures
highlighting module code... [ 96%] pdb2pqr.topology
highlighting module code... [100%] pdb2pqr.utilities

writing additional pages... search done
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 2 warnings.

The HTML pages are in build/html.
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_test -O--buildsystem=pybuild
I: pybuild base:275: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; python3.11 -m pytest tests
============================= test session starts ==============================
platform linux -- Python 3.11.4, pytest-7.2.1, pluggy-1.0.0+repack
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build, configfile: pytest.ini

----------------------------- live log collection ------------------------------
WARNING  py.warnings:warnings.py:109 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/tests/core_test.py:81: PytestUnknownMarkWarning: Unknown pytest.mark.long_test - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
  @pytest.mark.long_test

ERROR    regression_test:regression_test.py:173 Need to reinstate the --apbs-input test with a temporary directory as path
collected 316 items

tests/core_test.py::test_short_pdb[4E8M] 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[5D8V] SKIPPED (not running tests ...) [  1%]
tests/core_test.py::test_short_pdb[7BNA] 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[1FAS] SKIPPED (not running tests ...) [  2%]
tests/core_test.py::test_short_pdb[4UN3] SKIPPED (not running tests ...) [  2%]
tests/core_test.py::test_basic_cif[4E8M] SKIPPED (not running tests ...) [  2%]
tests/core_test.py::test_basic_cif[1AQO] 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[5D8V] SKIPPED (not running tests ...) [  3%]
tests/core_test.py::test_basic_cif[7BNA] SKIPPED (not running tests ...) [  4%]
tests/core_test.py::test_basic_cif[1K1I] 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[4UN3] SKIPPED (not running tests ...) [  5%]
tests/core_test.py::test_long_pdb[1BM8] SKIPPED (not running tests r...) [  5%]
tests/core_test.py::test_long_pdb[3RVC] SKIPPED (not running tests r...) [  5%]
tests/core_test.py::test_long_pdb[2NSN] SKIPPED (not running tests r...) [  6%]
tests/core_test.py::test_long_pdb[2PND] SKIPPED (not running tests r...) [  6%]
tests/core_test.py::test_long_pdb[1ZVA] SKIPPED (not running tests r...) [  6%]
tests/core_test.py::test_long_pdb[1NH9] SKIPPED (not running tests r...) [  6%]
tests/core_test.py::test_long_pdb[1B0X] SKIPPED (not running tests r...) [  7%]
tests/core_test.py::test_long_pdb[1H75] SKIPPED (not running tests r...) [  7%]
tests/core_test.py::test_long_pdb[2CMP] SKIPPED (not running tests r...) [  7%]
tests/core_test.py::test_long_pdb[2ZQE] SKIPPED (not running tests r...) [  8%]
tests/core_test.py::test_long_pdb[2SFA] SKIPPED (not running tests r...) [  8%]
tests/core_test.py::test_long_pdb[1OPC] SKIPPED (not running tests r...) [  8%]
tests/core_test.py::test_long_pdb[2FWG] SKIPPED (not running tests r...) [  9%]
tests/core_test.py::test_long_pdb[4AXT] SKIPPED (not running tests r...) [  9%]
tests/core_test.py::test_long_pdb[1KFN] SKIPPED (not running tests r...) [  9%]
tests/core_test.py::test_long_pdb[1JQ0] SKIPPED (not running tests r...) [ 10%]
tests/core_test.py::test_long_pdb[2D8E] SKIPPED (not running tests r...) [ 10%]
tests/core_test.py::test_long_pdb[4CFI] SKIPPED (not running tests r...) [ 10%]
tests/core_test.py::test_long_pdb[4GMQ] SKIPPED (not running tests r...) [ 11%]
tests/core_test.py::test_long_pdb[3WFV] SKIPPED (not running tests r...) [ 11%]
tests/core_test.py::test_long_pdb[2IBL] SKIPPED (not running tests r...) [ 11%]
tests/core_test.py::test_long_pdb[4G3O] SKIPPED (not running tests r...) [ 12%]
tests/core_test.py::test_long_pdb[1PDO] SKIPPED (not running tests r...) [ 12%]
tests/core_test.py::test_long_pdb[4HS2] SKIPPED (not running tests r...) [ 12%]
tests/core_test.py::test_long_pdb[3JTE] SKIPPED (not running tests r...) [ 12%]
tests/core_test.py::test_long_pdb[2NWD] SKIPPED (not running tests r...) [ 13%]
tests/core_test.py::test_long_pdb[1NXO] SKIPPED (not running tests r...) [ 13%]
tests/core_test.py::test_long_pdb[3ISU] SKIPPED (not running tests r...) [ 13%]
tests/core_test.py::test_long_pdb[2J6B] SKIPPED (not running tests r...) [ 14%]
tests/core_test.py::test_long_pdb[2X4J] SKIPPED (not running tests r...) [ 14%]
tests/core_test.py::test_long_pdb[4OSN] SKIPPED (not running tests r...) [ 14%]
tests/core_test.py::test_long_pdb[3I35] SKIPPED (not running tests r...) [ 15%]
tests/core_test.py::test_long_pdb[1HUF] SKIPPED (not running tests r...) [ 15%]
tests/core_test.py::test_long_pdb[1FAS] SKIPPED (not running tests r...) [ 15%]
tests/core_test.py::test_long_pdb[3H0X] SKIPPED (not running tests r...) [ 16%]
tests/core_test.py::test_long_pdb[4YPC] SKIPPED (not running tests r...) [ 16%]
tests/core_test.py::test_long_pdb[3CQT] SKIPPED (not running tests r...) [ 16%]
tests/core_test.py::test_long_pdb[2IWN] SKIPPED (not running tests r...) [ 17%]
tests/core_test.py::test_long_pdb[4NPN] SKIPPED (not running tests r...) [ 17%]
tests/core_test.py::test_long_pdb[4YKD] SKIPPED (not running tests r...) [ 17%]
tests/core_test.py::test_long_pdb[1R7J] SKIPPED (not running tests r...) [ 18%]
tests/core_test.py::test_long_pdb[3C97] SKIPPED (not running tests r...) [ 18%]
tests/core_test.py::test_long_pdb[2GUS] SKIPPED (not running tests r...) [ 18%]
tests/core_test.py::test_long_pdb[1TIG] SKIPPED (not running tests r...) [ 18%]
tests/core_test.py::test_long_pdb[1TGN] SKIPPED (not running tests r...) [ 19%]
tests/core_test.py::test_long_pdb[2OP6] SKIPPED (not running tests r...) [ 19%]
tests/core_test.py::test_long_pdb[2QVO] SKIPPED (not running tests r...) [ 19%]
tests/core_test.py::test_long_pdb[4CVD] SKIPPED (not running tests r...) [ 20%]
tests/core_test.py::test_long_pdb[3S0A] SKIPPED (not running tests r...) [ 20%]
tests/core_test.py::test_long_pdb[2FI9] SKIPPED (not running tests r...) [ 20%]
tests/core_test.py::test_long_pdb[1RIS] 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[1X6J] SKIPPED (not running tests r...) [ 21%]
tests/core_test.py::test_long_pdb[1PGX] SKIPPED (not running tests r...) [ 22%]
tests/core_test.py::test_long_pdb[2J70] SKIPPED (not running tests r...) [ 22%]
tests/core_test.py::test_long_pdb[4IL7] SKIPPED (not running tests r...) [ 22%]
tests/core_test.py::test_long_pdb[1E7G] SKIPPED (not running tests r...) [ 23%]
tests/core_test.py::test_long_pdb[1YZM] SKIPPED (not running tests r...) [ 23%]
tests/core_test.py::test_long_pdb[1R5Q] SKIPPED (not running tests r...) [ 23%]
tests/core_test.py::test_long_pdb[2TGI] SKIPPED (not running tests r...) [ 24%]
tests/core_test.py::test_long_pdb[2XXC] SKIPPED (not running tests r...) [ 24%]
tests/core_test.py::test_long_pdb[1YQB] SKIPPED (not running tests r...) [ 24%]
tests/core_test.py::test_long_pdb[1IS5] SKIPPED (not running tests r...) [ 25%]
tests/core_test.py::test_long_pdb[3KT2] SKIPPED (not running tests r...) [ 25%]
tests/core_test.py::test_long_pdb[3HRN] SKIPPED (not running tests r...) [ 25%]
tests/core_test.py::test_long_pdb[4EO0] SKIPPED (not running tests r...) [ 25%]
tests/core_test.py::test_long_pdb[3ZZP] SKIPPED (not running tests r...) [ 26%]
tests/core_test.py::test_long_pdb[4ZMK] SKIPPED (not running tests r...) [ 26%]
tests/core_test.py::test_long_pdb[3IDW] SKIPPED (not running tests r...) [ 26%]
tests/core_test.py::test_long_pdb[1USM] SKIPPED (not running tests r...) [ 27%]
tests/core_test.py::test_long_pdb[4LJ1] SKIPPED (not running tests r...) [ 27%]
tests/core_test.py::test_long_pdb[2VWR] SKIPPED (not running tests r...) [ 27%]
tests/core_test.py::test_long_pdb[3B7H] SKIPPED (not running tests r...) [ 28%]
tests/core_test.py::test_long_pdb[1L2P] SKIPPED (not running tests r...) [ 28%]
tests/core_test.py::test_long_pdb[3FH2] SKIPPED (not running tests r...) [ 28%]
tests/core_test.py::test_long_pdb[1RJ1] SKIPPED (not running tests r...) [ 29%]
tests/core_test.py::test_long_pdb[2H2C] SKIPPED (not running tests r...) [ 29%]
tests/core_test.py::test_long_pdb[1USE] SKIPPED (not running tests r...) [ 29%]
tests/core_test.py::test_long_pdb[5V0O] SKIPPED (not running tests r...) [ 30%]
tests/core_test.py::test_long_pdb[3LMO] SKIPPED (not running tests r...) [ 30%]
tests/core_test.py::test_long_pdb[1DF4] SKIPPED (not running tests r...) [ 30%]
tests/core_test.py::test_long_pdb[3QC7] SKIPPED (not running tests r...) [ 31%]
tests/core_test.py::test_long_pdb[2GZV] SKIPPED (not running tests r...) [ 31%]
tests/core_test.py::test_long_pdb[1UG4] SKIPPED (not running tests r...) [ 31%]
tests/core_test.py::test_long_pdb[3ONJ] SKIPPED (not running tests r...) [ 31%]
tests/core_test.py::test_long_pdb[1TG0] SKIPPED (not running tests r...) [ 32%]
tests/core_test.py::test_long_pdb[4HTI] SKIPPED (not running tests r...) [ 32%]
tests/core_test.py::test_long_pdb[1TEN] SKIPPED (not running tests r...) [ 32%]
tests/core_test.py::test_long_pdb[2P5K] SKIPPED (not running tests r...) [ 33%]
tests/core_test.py::test_long_pdb[3RFI] SKIPPED (not running tests r...) [ 33%]
tests/core_test.py::test_long_pdb[1SJV] SKIPPED (not running tests r...) [ 33%]
tests/core_test.py::test_long_pdb[3HRO] SKIPPED (not running tests r...) [ 34%]
tests/core_test.py::test_long_pdb[1OPS] SKIPPED (not running tests r...) [ 34%]
tests/core_test.py::test_long_pdb[1HOE] SKIPPED (not running tests r...) [ 34%]
tests/core_test.py::test_long_pdb[2ERA] SKIPPED (not running tests r...) [ 35%]
tests/core_test.py::test_long_pdb[3QE1] SKIPPED (not running tests r...) [ 35%]
tests/core_test.py::test_long_pdb[1PHT] SKIPPED (not running tests r...) [ 35%]
tests/core_test.py::test_long_pdb[1WOU] SKIPPED (not running tests r...) [ 36%]
tests/core_test.py::test_long_pdb[4S11] SKIPPED (not running tests r...) [ 36%]
tests/core_test.py::test_long_pdb[2FD4] SKIPPED (not running tests r...) [ 36%]
tests/core_test.py::test_long_pdb[4L9E] SKIPPED (not running tests r...) [ 37%]
tests/core_test.py::test_long_pdb[1XAK] SKIPPED (not running tests r...) [ 37%]
tests/core_test.py::test_long_pdb[2JCP] SKIPPED (not running tests r...) [ 37%]
tests/core_test.py::test_long_pdb[1NKD] SKIPPED (not running tests r...) [ 37%]
tests/core_test.py::test_long_pdb[2SGA] SKIPPED (not running tests r...) [ 38%]
tests/core_test.py::test_long_pdb[2IGD] SKIPPED (not running tests r...) [ 38%]
tests/core_test.py::test_long_pdb[1P1L] SKIPPED (not running tests r...) [ 38%]
tests/core_test.py::test_long_pdb[1ZLM] SKIPPED (not running tests r...) [ 39%]
tests/core_test.py::test_long_pdb[2OO2] SKIPPED (not running tests r...) [ 39%]
tests/core_test.py::test_long_pdb[1I2T] SKIPPED (not running tests r...) [ 39%]
tests/core_test.py::test_long_pdb[3RJS] SKIPPED (not running tests r...) [ 40%]
tests/core_test.py::test_long_pdb[1LN4] SKIPPED (not running tests r...) [ 40%]
tests/core_test.py::test_long_pdb[2CGQ] SKIPPED (not running tests r...) [ 40%]
tests/core_test.py::test_long_pdb[3LS0] SKIPPED (not running tests r...) [ 41%]
tests/core_test.py::test_long_pdb[2ERW] SKIPPED (not running tests r...) [ 41%]
tests/core_test.py::test_long_pdb[3T8R] SKIPPED (not running tests r...) [ 41%]
tests/core_test.py::test_long_pdb[2YXF] SKIPPED (not running tests r...) [ 42%]
tests/core_test.py::test_long_pdb[4O7Q] SKIPPED (not running tests r...) [ 42%]
tests/core_test.py::test_long_pdb[3CSR] 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[1TVQ] SKIPPED (not running tests r...) [ 43%]
tests/core_test.py::test_long_pdb[2G7O] SKIPPED (not running tests r...) [ 43%]
tests/core_test.py::test_long_pdb[4ZQA] SKIPPED (not running tests r...) [ 43%]
tests/core_test.py::test_long_pdb[2R6Q] SKIPPED (not running tests r...) [ 44%]
tests/core_test.py::test_long_pdb[3DVI] SKIPPED (not running tests r...) [ 44%]
tests/core_test.py::test_long_pdb[2NYC] SKIPPED (not running tests r...) [ 44%]
tests/core_test.py::test_long_pdb[3KZD] SKIPPED (not running tests r...) [ 45%]
tests/core_test.py::test_long_pdb[2FRG] SKIPPED (not running tests r...) [ 45%]
tests/core_test.py::test_long_pdb[3NGP] SKIPPED (not running tests r...) [ 45%]
tests/core_test.py::test_long_pdb[2YGS] SKIPPED (not running tests r...) [ 46%]
tests/core_test.py::test_long_pdb[1OX3] SKIPPED (not running tests r...) [ 46%]
tests/core_test.py::test_long_pdb[3ZSL] SKIPPED (not running tests r...) [ 46%]
tests/core_test.py::test_long_pdb[4CRH] SKIPPED (not running tests r...) [ 47%]
tests/core_test.py::test_long_pdb[1TQG] SKIPPED (not running tests r...) [ 47%]
tests/core_test.py::test_long_pdb[2PII] SKIPPED (not running tests r...) [ 47%]
tests/core_test.py::test_long_pdb[4GQM] SKIPPED (not running tests r...) [ 48%]
tests/core_test.py::test_long_pdb[2IVY] SKIPPED (not running tests r...) [ 48%]
tests/core_test.py::test_long_pdb[1DUP] SKIPPED (not running tests r...) [ 48%]
tests/core_test.py::test_long_pdb[4PGR] SKIPPED (not running tests r...) [ 49%]
tests/core_test.py::test_long_pdb[3ZHI] SKIPPED (not running tests r...) [ 49%]
tests/core_test.py::test_long_pdb[2OCH] SKIPPED (not running tests r...) [ 49%]
tests/core_test.py::test_long_pdb[1J27] SKIPPED (not running tests r...) [ 50%]
tests/core_test.py::test_long_pdb[1ZX6] SKIPPED (not running tests r...) [ 50%]
tests/core_test.py::test_long_pdb[4RWU] SKIPPED (not running tests r...) [ 50%]
tests/core_test.py::test_long_pdb[4GS3] SKIPPED (not running tests r...) [ 50%]
tests/core_test.py::test_long_pdb[1X3O] SKIPPED (not running tests r...) [ 51%]
tests/core_test.py::test_long_pdb[1ZZK] SKIPPED (not running tests r...) [ 51%]
tests/core_test.py::test_long_pdb[1V2Z] SKIPPED (not running tests r...) [ 51%]
tests/core_test.py::test_long_pdb[3V1A] SKIPPED (not running tests r...) [ 52%]
tests/core_test.py::test_long_pdb[4I2T] SKIPPED (not running tests r...) [ 52%]
tests/core_test.py::test_long_pdb[1NOA] SKIPPED (not running tests r...) [ 52%]
tests/core_test.py::test_long_pdb[3NX6] SKIPPED (not running tests r...) [ 53%]
tests/core_test.py::test_long_pdb[3CE7] SKIPPED (not running tests r...) [ 53%]
tests/core_test.py::test_long_pdb[2ESK] SKIPPED (not running tests r...) [ 53%]
tests/core_test.py::test_long_pdb[1J2A] SKIPPED (not running tests r...) [ 54%]
tests/core_test.py::test_long_pdb[2EBB] SKIPPED (not running tests r...) [ 54%]
tests/core_test.py::test_long_pdb[2JIC] SKIPPED (not running tests r...) [ 54%]
tests/core_test.py::test_long_pdb[1TUD] SKIPPED (not running tests r...) [ 55%]
tests/core_test.py::test_long_pdb[3CP1] SKIPPED (not running tests r...) [ 55%]
tests/core_test.py::test_long_pdb[2HDZ] SKIPPED (not running tests r...) [ 55%]
tests/core_test.py::test_long_pdb[4N6T] SKIPPED (not running tests r...) [ 56%]
tests/core_test.py::test_long_pdb[2BYG] SKIPPED (not running tests r...) [ 56%]
tests/core_test.py::test_long_pdb[3TSV] SKIPPED (not running tests r...) [ 56%]
tests/core_test.py::test_long_pdb[3I1G] SKIPPED (not running tests r...) [ 56%]
tests/core_test.py::test_long_pdb[2PCY] 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[3T1S] SKIPPED (not running tests r...) [ 57%]
tests/core_test.py::test_long_pdb[1AIL] SKIPPED (not running tests r...) [ 58%]
tests/core_test.py::test_long_pdb[1P9I] SKIPPED (not running tests r...) [ 58%]
tests/core_test.py::test_long_pdb[4TTW] SKIPPED (not running tests r...) [ 58%]
tests/core_test.py::test_long_pdb[2CWR] SKIPPED (not running tests r...) [ 59%]
tests/core_test.py::test_long_pdb[3SO2] SKIPPED (not running tests r...) [ 59%]
tests/core_test.py::test_long_pdb[4Q2Q] SKIPPED (not running tests r...) [ 59%]
tests/core_test.py::test_long_pdb[2PTV] SKIPPED (not running tests r...) [ 60%]
tests/core_test.py::test_long_pdb[2REY] SKIPPED (not running tests r...) [ 60%]
tests/core_test.py::test_long_pdb[1AFS] SKIPPED (not running tests r...) [ 60%]
tests/core_test.py::test_long_pdb[1PZC] SKIPPED (not running tests r...) [ 61%]
tests/core_test.py::test_long_pdb[2HC8] SKIPPED (not running tests r...) [ 61%]
tests/core_test.py::test_long_pdb[3LAA] SKIPPED (not running tests r...) [ 61%]
tests/core_test.py::test_long_pdb[2HP7] SKIPPED (not running tests r...) [ 62%]
tests/core_test.py::test_long_pdb[5DV8] SKIPPED (not running tests r...) [ 62%]
tests/core_test.py::test_long_pdb[2CJJ] SKIPPED (not running tests r...) [ 62%]
tests/core_test.py::test_long_pdb[2QR3] SKIPPED (not running tests r...) [ 62%]
tests/core_test.py::test_long_pdb[2PMR] SKIPPED (not running tests r...) [ 63%]
tests/core_test.py::test_long_pdb[3LLB] SKIPPED (not running tests r...) [ 63%]
tests/core_test.py::test_long_pdb[5EE2] SKIPPED (not running tests r...) [ 63%]
tests/core_test.py::test_long_pdb[2CKX] SKIPPED (not running tests r...) [ 64%]
tests/core_test.py::test_long_pdb[1OA4] SKIPPED (not running tests r...) [ 64%]
tests/core_test.py::test_long_pdb[2QBV] SKIPPED (not running tests r...) [ 64%]
tests/core_test.py::test_long_pdb[1Z0P] SKIPPED (not running tests r...) [ 65%]
tests/core_test.py::test_long_pdb[1X91] SKIPPED (not running tests r...) [ 65%]
tests/core_test.py::test_long_pdb[3RFF] SKIPPED (not running tests r...) [ 65%]
tests/core_test.py::test_long_pdb[3US6] SKIPPED (not running tests r...) [ 66%]
tests/core_test.py::test_broken_backbone[1EJG] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-buildd/pytest-0/test_broken_backbone_1EJG_0/1EJG.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG
XFAIL                                                                    [ 66%]
tests/core_test.py::test_broken_backbone[4MGP] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-buildd/pytest-0/test_broken_backbone_4MGP_0/4MGP.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP
XFAIL                                                                    [ 66%]
tests/core_test.py::test_broken_backbone[2V75] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-buildd/pytest-0/test_broken_backbone_2V75_0/2V75.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75
XFAIL                                                                    [ 67%]
tests/core_test.py::test_broken_backbone[3U7T] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-buildd/pytest-0/test_broken_backbone_3U7T_0/3U7T.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T
XFAIL                                                                    [ 67%]
tests/core_test.py::test_protonated_terminals[C-terminal HID] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-buildd/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber).
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output.
INFO     common:common.py:198 0 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 67%]
tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-buildd/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
INFO     PDB2PQR3.6.1:main.py:459 This biomolecule is clean.  No repair needed.
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber).
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output.
INFO     common:common.py:198 0 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 68%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 68%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 68%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 68%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED     [ 69%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 69%]
tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED           [ 69%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 70%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 70%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 70%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 71%]
tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED     [ 71%]
tests/io_test.py::test_read_pqr[tests/data/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_whitespace_ff=PEOEPB.pqr] PASSED [ 72%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.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 [ 73%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 73%]
tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 73%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 74%]
tests/io_test.py::test_read_qcd PASSED                                   [ 74%]
tests/io_test.py::test_dx2cube 
-------------------------------- live log call ---------------------------------
INFO     io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr...
INFO     io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx...
INFO     io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-buildd/pytest-0/test_dx2cube0/test.cube...
INFO     io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-buildd/pytest-0/test_dx2cube0/test.cube...
INFO     io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube...
INFO     io_test:io_test.py:68 No differences found in output
PASSED                                                                   [ 74%]
tests/ligand_test.py::test_peoe_charges 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
PASSED                                                                   [ 75%]
tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 ->  0.00
PASSED                                                                   [ 75%]
tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 -> -0.00
PASSED                                                                   [ 75%]
tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
INFO     ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00
PASSED                                                                   [ 75%]
tests/ligand_test.py::test_assign_parameters[acetate.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00
PASSED                                                                   [ 76%]
tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 -> -0.00
PASSED                                                                   [ 76%]
tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type.
WARNING  pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type.
INFO     ligand_test:ligand_test.py:73 Total charge:  1.00 ->  1.00
PASSED                                                                   [ 76%]
tests/ligand_test.py::test_assign_parameters[adp.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order.
INFO     ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00
PASSED                                                                   [ 77%]
tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 -> -0.00
PASSED                                                                   [ 77%]
tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 ->  0.00
PASSED                                                                   [ 77%]
tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 ->  0.00
PASSED                                                                   [ 78%]
tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00
PASSED                                                                   [ 78%]
tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 ->  0.00
PASSED                                                                   [ 78%]
tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 -> -0.00
PASSED                                                                   [ 79%]
tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 ->  0.00
PASSED                                                                   [ 79%]
tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type.
WARNING  pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type.
INFO     ligand_test:ligand_test.py:73 Total charge:  1.00 ->  1.00
PASSED                                                                   [ 79%]
tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
PASSED                                                                   [ 80%]
tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
PASSED                                                                   [ 80%]
tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
PASSED                                                                   [ 80%]
tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED            [ 81%]
tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED       [ 81%]
tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type.
PASSED                                                                   [ 81%]
tests/ligand_test.py::test_formal_charge[adp.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order.
PASSED                                                                   [ 81%]
tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED         [ 82%]
tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED        [ 82%]
tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED            [ 82%]
tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED         [ 83%]
tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED           [ 83%]
tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED        [ 83%]
tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED            [ 84%]
tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type.
PASSED                                                                   [ 84%]
tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED           [ 84%]
tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED                 [ 85%]
tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED                 [ 85%]
tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED     [ 85%]
tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED                [ 86%]
tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED             [ 86%]
tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED                [ 86%]
tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED                [ 87%]
tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED                [ 87%]
tests/ligand_test.py::test_rings[acetate.mol2] PASSED                    [ 87%]
tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED               [ 87%]
tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED              [ 88%]
tests/ligand_test.py::test_rings[adp.mol2] PASSED                        [ 88%]
tests/ligand_test.py::test_rings[anthracene.mol2] PASSED                 [ 88%]
tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED                [ 89%]
tests/ligand_test.py::test_rings[ethanol.mol2] PASSED                    [ 89%]
tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED                 [ 89%]
tests/ligand_test.py::test_rings[glycerol.mol2] PASSED                   [ 90%]
tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED                [ 90%]
tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED                    [ 90%]
tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED        [ 91%]
tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%]
tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%]
tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%]
tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%]
tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%]
tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%]
tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%]
tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%]
tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%]
tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%]
tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%]
tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%]
tests/regression_test.py::test_basic[1AFS basic local] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-buildd/pytest-0/test_basic_1AFS_basic_local_0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES.  Parsing as new residue.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333
WARNING  pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
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-buildd/pytest-0/test_forcefields_1AFS_whitespa0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES.  Parsing as new residue.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
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-buildd/pytest-0/test_forcefields_1AFS_whitespa1/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
WARNING  pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 5 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
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-buildd/pytest-0/test_forcefields_1AFS_whitespa2/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
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-buildd/pytest-0/test_forcefields_1AFS_whitespa3/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
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-buildd/pytest-0/test_forcefields_1AFS_whitespa4/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
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-buildd/pytest-0/test_forcefields_1AFS_whitespa5/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
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-buildd/pytest-0/test_other_options_1AFS_whites0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps.
INFO     common:common.py:198 0 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
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-buildd/pytest-0/test_other_options_1A1P_assign0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output.
INFO     common:common.py:198 0 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
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-buildd/pytest-0/test_other_options_1A1P_nodebu0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
INFO     PDB2PQR3.6.1:main.py:459 This biomolecule is clean.  No repair needed.
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization...
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output.
INFO     common:common.py:198 0 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
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-buildd/pytest-0/test_other_options_1AFS_chain_0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
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-buildd/pytest-0/test_other_options_1AFS_neutra0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
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-buildd/pytest-0/test_other_options_1AFS_drop_w0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:768 Dropping water from structure.
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
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-buildd/pytest-0/test_other_options_1AFS_userff0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 99%]
tests/test_version.py::test_version_exists PASSED                        [ 99%]
tests/test_version.py::test_version PASSED                               [100%]

=============================== warnings summary ===============================
../../../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:121
  /usr/lib/python3/dist-packages/pkg_resources/__init__.py:121: DeprecationWarning: pkg_resources is deprecated as an API
    warnings.warn("pkg_resources is deprecated as an API", DeprecationWarning)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
======= 92 passed, 220 skipped, 4 xfailed, 1 warning in 64.95s (0:01:04) =======
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=pybuild
   dh_prep -O--buildsystem=pybuild
   dh_installdirs -O--buildsystem=pybuild
   dh_auto_install -O--buildsystem=pybuild
I: pybuild base:275: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/debian/tmp 
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer, pypa/build or
        other standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
running build
running build_py
running install_lib
creating /<<PKGBUILDDIR>>/debian/tmp/usr
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/.pytest_cache/CACHEDIR.TAG -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/.pytest_cache/.gitignore -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v/cache
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/.pytest_cache/v/cache/stepwise -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v/cache
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/.pytest_cache/v/cache/nodeids -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v/cache
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/.pytest_cache/README.md -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/run.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/psize.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/residue.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/biomolecule.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/quatfit.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/config.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/inputgen.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__main__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/definitions.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/pdb.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/debump.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/main.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/forcefield.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/structures.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/structures.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/optimize.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/optimize.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/structures.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/topology.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/cif.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/peoe.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/mol2.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/topology.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/mol2.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/peoe.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/utilities.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/na.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/residue.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/utilities.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/forcefield.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/cif.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/biomolecule.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/psize.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/_version.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/inputgen.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/pdb.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/structures.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/main.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/definitions.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/debump.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/aa.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/io.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/cells.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/na.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/quatfit.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/config.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/aa.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/_version.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
creating /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/CHARMM.DAT -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AMBER.DAT -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TOPOLOGY.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PARSE.names -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AMBER.names -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PEOEPB.DAT -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PARSE.DAT -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/HYDROGENS.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PEOEPB.names -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/SWANSON.DAT -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PATCHES.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/SWANSON.names -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/CHARMM.names -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/NA.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TYL06.names -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AA.xml -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TYL06.DAT -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/__init__.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/cells.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pdb2pqr/io.py -> /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/run.py to run.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/psize.py to psize.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/residue.py to residue.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/biomolecule.py to biomolecule.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/quatfit.py to quatfit.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/config.py to config.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/inputgen.py to inputgen.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__main__.py to __main__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/definitions.py to definitions.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/pdb.py to pdb.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/debump.py to debump.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/main.py to main.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/forcefield.py to forcefield.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/structures.py to structures.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/optimize.py to optimize.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/structures.py to structures.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/topology.py to topology.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/cif.py to cif.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/peoe.py to peoe.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/mol2.py to mol2.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/topology.py to topology.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/utilities.py to utilities.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/na.py to na.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/aa.py to aa.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/_version.py to _version.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/cells.py to cells.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/io.py to io.cpython-311.pyc
running install_egg_info
running egg_info
creating pdb2pqr.egg-info
writing pdb2pqr.egg-info/PKG-INFO
writing dependency_links to pdb2pqr.egg-info/dependency_links.txt
writing entry points to pdb2pqr.egg-info/entry_points.txt
writing requirements to pdb2pqr.egg-info/requires.txt
writing top-level names to pdb2pqr.egg-info/top_level.txt
writing manifest file 'pdb2pqr.egg-info/SOURCES.txt'
reading manifest file 'pdb2pqr.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'pdb2pka'
adding license file 'LICENSE.md'
adding license file 'COPYING'
writing manifest file 'pdb2pqr.egg-info/SOURCES.txt'
Copying pdb2pqr.egg-info to /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr-3.6.1.egg-info
Skipping SOURCES.txt
running install_scripts
Installing dx2cube script to /<<PKGBUILDDIR>>/debian/tmp/usr/bin
Installing inputgen script to /<<PKGBUILDDIR>>/debian/tmp/usr/bin
Installing pdb2pqr script to /<<PKGBUILDDIR>>/debian/tmp/usr/bin
Installing pdb2pqr30 script to /<<PKGBUILDDIR>>/debian/tmp/usr/bin
   dh_install -O--buildsystem=pybuild
   debian/rules override_dh_installdocs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installdocs
dh_installdocs -p pdb2pqr-doc --doc-main-package pdb2pqr build/html
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_sphinxdoc -O--buildsystem=pybuild
   dh_installchangelogs -O--buildsystem=pybuild
   dh_installexamples -O--buildsystem=pybuild
   debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/dx2cube --no-info --version-string 3.6.1+dfsg > dx2cube.1
PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/inputgen --no-info --version-string 3.6.1+dfsg > inputgen.1
PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/pdb2pqr30 --no-info --version-string 3.6.1+dfsg > pdb2pqr30.1
dh_installman
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_python3 -O--buildsystem=pybuild
   dh_installsystemduser -O--buildsystem=pybuild
   dh_perl -O--buildsystem=pybuild
   dh_link -O--buildsystem=pybuild
   dh_strip_nondeterminism -O--buildsystem=pybuild
   dh_compress -O--buildsystem=pybuild
   dh_fixperms -O--buildsystem=pybuild
   dh_missing -O--buildsystem=pybuild
   dh_installdeb -O--buildsystem=pybuild
   dh_gencontrol -O--buildsystem=pybuild
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
INFO: pkgstriptranslations version 153
INFO: pkgstriptranslations version 153
INFO: pkgstriptranslations version 153
pkgstriptranslations: processing python3-pdb2pqr (in debian/python3-pdb2pqr); do_strip: , oemstrip: 
pkgstriptranslations: processing pdb2pqr-doc (in debian/pdb2pqr-doc); do_strip: , oemstrip: 
pkgstriptranslations: processing pdb2pqr (in debian/pdb2pqr); do_strip: , oemstrip: 
pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
pkgstripfiles: processing control file: debian/python3-pdb2pqr/DEBIAN/control, package python3-pdb2pqr, directory debian/python3-pdb2pqr
INFO: pkgstripfiles: waiting for lock (python3-pdb2pqr) ...
pkgstripfiles: processing control file: debian/pdb2pqr/DEBIAN/control, package pdb2pqr, directory debian/pdb2pqr
Searching for duplicated docs in dependency python3-pdb2pqr...
  symlinking changelog.Debian.gz in pdb2pqr to file in python3-pdb2pqr
pkgstripfiles: Running PNG optimization (using 4 cpus) for package pdb2pqr ...
pkgstripfiles: No PNG files.
dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_3.6.1+dfsg-1_all.deb'.
INFO: pkgstripfiles: waiting for lock (python3-pdb2pqr) ...
INFO: pkgstripfiles: waiting for lock (python3-pdb2pqr) ...
INFO: pkgstripfiles: waiting for lock (python3-pdb2pqr) ...
INFO: pkgstripfiles: waiting for lock (python3-pdb2pqr) ...
pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
pkgstripfiles: processing control file: debian/pdb2pqr-doc/DEBIAN/control, package pdb2pqr-doc, directory debian/pdb2pqr-doc
pkgstripfiles: Disabled PNG optimization for -doc package pdb2pqr-doc (to save build time)
dpkg-deb: building package 'pdb2pqr-doc' in '../pdb2pqr-doc_3.6.1+dfsg-1_all.deb'.
pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-pdb2pqr ...
pkgstripfiles: No PNG files.
dpkg-deb: building package 'python3-pdb2pqr' in '../python3-pdb2pqr_3.6.1+dfsg-1_all.deb'.
 dpkg-genbuildinfo --build=binary -O../pdb2pqr_3.6.1+dfsg-1_amd64.buildinfo
 dpkg-genchanges --build=binary -mLaunchpad Build Daemon <buildd@lcy02-amd64-117.buildd> -O../pdb2pqr_3.6.1+dfsg-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2023-06-12T23:17:01Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


pdb2pqr_3.6.1+dfsg-1_amd64.changes:
-----------------------------------

Format: 1.8
Date: Mon, 12 Jun 2023 23:05:08 +0530
Source: pdb2pqr
Binary: pdb2pqr pdb2pqr-doc python3-pdb2pqr
Built-For-Profiles: noudeb
Architecture: all
Version: 3.6.1+dfsg-1
Distribution: mantic-proposed
Urgency: medium
Maintainer: Launchpad Build Daemon <buildd@lcy02-amd64-117.buildd>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
 pdb2pqr    - Preparation of protein structures for electrostatics calculations
 pdb2pqr-doc - example files accompanying pdb2pqr
 python3-pdb2pqr - Preparation of protein structures for electrostatics calculations
Changes:
 pdb2pqr (3.6.1+dfsg-1) unstable; urgency=medium
 .
   * Team Upload.
   * New upstream version 3.6.1+dfsg
   * Update patch to skip propka network test
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Distribution field may be wrong!!!
+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: pdb2pqr
Binary: pdb2pqr pdb2pqr-doc python3-pdb2pqr
Architecture: all
Version: 3.6.1+dfsg-1
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Build-Origin: Ubuntu
Build-Architecture: amd64
Build-Date: Mon, 12 Jun 2023 23:17:00 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
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Installed-Build-Depends:
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 autopoint (= 0.21-12),
 autotools-dev (= 20220109.1),
 base-files (= 12.3ubuntu3),
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 libc-bin (= 2.37-0ubuntu2),
 libc-dev-bin (= 2.37-0ubuntu2),
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 libcom-err2 (= 1.47.0-1ubuntu1),
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 libcrypt1 (= 1:4.4.35-1),
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 libdebconfclient0 (= 0.267ubuntu1),
 libdebhelper-perl (= 13.11.4ubuntu3),
 libdpkg-perl (= 1.21.22ubuntu1),
 libdw1 (= 0.188-2.1),
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 libexpat1-dev (= 2.5.0-1),
 libffi8 (= 3.4.4-1),
 libfile-stripnondeterminism-perl (= 1.13.1-1),
 libgcc-12-dev (= 12.3.0-1ubuntu1),
 libgcc-s1 (= 13.1.0-2ubuntu2),
 libgcrypt20 (= 1.10.1-3ubuntu1),
 libgdbm-compat4 (= 1.23-3),
 libgdbm6 (= 1.23-3),
 libgfortran5 (= 13.1.0-2ubuntu2),
 libgmp10 (= 2:6.2.1+dfsg1-1.1ubuntu1),
 libgomp1 (= 13.1.0-2ubuntu2),
 libgpg-error0 (= 1.46-1),
 libgprofng0 (= 2.40-2ubuntu6),
 libgssapi-krb5-2 (= 1.20.1-2),
 libicu72 (= 72.1-3ubuntu2),
 libisl23 (= 0.26-2),
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 libjansson4 (= 2.14-2),
 libjs-jquery (= 3.6.1+dfsg+~3.5.14-1),
 libjs-sphinxdoc (= 5.3.0-4),
 libjs-underscore (= 1.13.4~dfsg+~1.11.4-3),
 libjson-perl (= 4.10000-1),
 libk5crypto3 (= 1.20.1-2),
 libkeyutils1 (= 1.6.3-2),
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 libkrb5support0 (= 1.20.1-2),
 liblapack3 (= 3.11.0-2),
 liblocale-gettext-perl (= 1.07-5),
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 liblzma5 (= 5.4.1-0.2),
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 libmagic1 (= 1:5.44-3),
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 libmpc3 (= 1.3.1-1),
 libmpfr6 (= 4.2.0-1),
 libncursesw6 (= 6.4-4),
 libnsl-dev (= 1.3.0-2build2),
 libnsl2 (= 1.3.0-2build2),
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 libpam-modules-bin (= 1.5.2-6ubuntu1),
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 libpcre2-8-0 (= 10.42-1),
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 libpipeline1 (= 1.5.7-1),
 libpython3-dev (= 3.11.2-1),
 libpython3-stdlib (= 3.11.2-1),
 libpython3.11 (= 3.11.4-1),
 libpython3.11-dev (= 3.11.4-1),
 libpython3.11-minimal (= 3.11.4-1),
 libpython3.11-stdlib (= 3.11.4-1),
 libquadmath0 (= 13.1.0-2ubuntu2),
 libreadline8 (= 8.2-1.3),
 libseccomp2 (= 2.5.4-1ubuntu3),
 libselinux1 (= 3.4-1build4),
 libsmartcols1 (= 2.38.1-5ubuntu2),
 libsqlite3-0 (= 3.40.1-2),
 libssl3 (= 3.0.9-1ubuntu1),
 libstdc++-12-dev (= 12.3.0-1ubuntu1),
 libstdc++6 (= 13.1.0-2ubuntu2),
 libsub-override-perl (= 0.09-4),
 libsystemd0 (= 252.5-2ubuntu3),
 libtinfo6 (= 6.4-4),
 libtirpc-common (= 1.3.3+ds-1),
 libtirpc-dev (= 1.3.3+ds-1),
 libtirpc3 (= 1.3.3+ds-1),
 libtool (= 2.4.7-5),
 libtsan2 (= 13.1.0-2ubuntu2),
 libubsan1 (= 13.1.0-2ubuntu2),
 libuchardet0 (= 0.0.7-1build2),
 libudev1 (= 252.5-2ubuntu3),
 libunistring2 (= 1.0-2),
 libuuid1 (= 2.38.1-5ubuntu2),
 libxml2 (= 2.9.14+dfsg-1.2),
 libzstd1 (= 1.5.4+dfsg2-5),
 linux-libc-dev (= 6.3.0-7.7),
 login (= 1:4.13+dfsg1-1ubuntu1),
 lto-disabled-list (= 41),
 m4 (= 1.4.19-3),
 make (= 4.3-4.1build1),
 man-db (= 2.11.2-2),
 mawk (= 1.3.4.20200120-3.1),
 media-types (= 10.0.0),
 ncurses-base (= 6.4-4),
 ncurses-bin (= 6.4-4),
 openssl (= 3.0.9-1ubuntu1),
 patch (= 2.7.6-7build2),
 perl (= 5.36.0-7ubuntu1),
 perl-base (= 5.36.0-7ubuntu1),
 perl-modules-5.36 (= 5.36.0-7ubuntu1),
 po-debconf (= 1.0.21+nmu1),
 python-babel-localedata (= 2.10.3-1),
 python3 (= 3.11.2-1),
 python3-alabaster (= 0.7.12-1),
 python3-attr (= 22.2.0-1),
 python3-babel (= 2.10.3-1),
 python3-certifi (= 2022.9.24-1),
 python3-chardet (= 5.1.0+dfsg-2),
 python3-dateutil (= 2.8.2-2),
 python3-dev (= 3.11.2-1),
 python3-distutils (= 3.11.4-1),
 python3-docutils (= 0.19+dfsg-6),
 python3-idna (= 3.3-1),
 python3-imagesize (= 1.4.1-1),
 python3-iniconfig (= 1.1.1-2),
 python3-jinja2 (= 3.1.2-1),
 python3-lib2to3 (= 3.11.4-1),
 python3-markupsafe (= 2.1.2-1build1),
 python3-minimal (= 3.11.2-1),
 python3-more-itertools (= 8.10.0-2),
 python3-numpy (= 1:1.24.2-1),
 python3-packaging (= 23.1-1),
 python3-pandas (= 1.5.3+dfsg-2),
 python3-pandas-lib (= 1.5.3+dfsg-2),
 python3-pdbx (= 2.0.1-2),
 python3-pkg-resources (= 67.8.0-1),
 python3-pluggy (= 1.0.0+repack-1),
 python3-propka (= 3.5.0-1),
 python3-py (= 1.11.0-1),
 python3-pygments (= 2.15.1+dfsg-1),
 python3-pytest (= 7.2.1-2),
 python3-requests (= 2.28.1+dfsg-1ubuntu2),
 python3-roman (= 3.3-3),
 python3-setuptools (= 67.8.0-1),
 python3-six (= 1.16.0-4),
 python3-snowballstemmer (= 2.2.0-4),
 python3-sphinx (= 5.3.0-4),
 python3-sphinx-rtd-theme (= 1.2.0+dfsg-1),
 python3-testfixtures (= 7.0.4-1),
 python3-tz (= 2023.3-2),
 python3-urllib3 (= 1.26.12-1),
 python3.11 (= 3.11.4-1),
 python3.11-dev (= 3.11.4-1),
 python3.11-minimal (= 3.11.4-1),
 readline-common (= 8.2-1.3),
 rpcsvc-proto (= 1.4.2-0ubuntu6),
 sed (= 4.9-1),
 sensible-utils (= 0.0.17+nmu1),
 sgml-base (= 1.31),
 sphinx-common (= 5.3.0-4),
 sphinx-rtd-theme-common (= 1.2.0+dfsg-1),
 sysvinit-utils (= 3.06-4ubuntu1),
 tar (= 1.34+dfsg-1.2ubuntu1),
 tzdata (= 2023c-4exp1ubuntu1),
 usrmerge (= 35ubuntu1),
 util-linux (= 2.38.1-5ubuntu2),
 util-linux-extra (= 2.38.1-5ubuntu2),
 xml-core (= 0.18+nmu1),
 xz-utils (= 5.4.1-0.2),
 zlib1g (= 1:1.2.13.dfsg-1ubuntu4),
 zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu4)
Environment:
 DEB_BUILD_OPTIONS="parallel=4"
 DEB_BUILD_PROFILES="noudeb"
 LANG="C.UTF-8"
 LC_ALL="C.UTF-8"
 SOURCE_DATE_EPOCH="1686591308"


+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


pdb2pqr-doc_3.6.1+dfsg-1_all.deb
--------------------------------

 new Debian package, version 2.0.
 size 258234 bytes: control archive=3876 bytes.
     675 bytes,    17 lines      control              
   10750 bytes,   127 lines      md5sums              
 Package: pdb2pqr-doc
 Source: pdb2pqr
 Version: 3.6.1+dfsg-1
 Architecture: all
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 4230
 Depends: libjs-sphinxdoc (>= 5.2), sphinx-rtd-theme-common (>= 1.2.0+dfsg)
 Recommends: pdb2pqr
 Section: doc
 Priority: optional
 Multi-Arch: foreign
 Homepage: https://www.poissonboltzmann.org
 Description: example files accompanying pdb2pqr
  Files containing protein structures tend to become large very quickly and
  most users of this package will refrain from their installation, particularly
  on larger clusters.

drwxr-xr-x root/root         0 2023-06-12 17:35 ./
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/doc-base/
-rw-r--r-- root/root       258 2023-06-12 17:29 ./usr/share/doc-base/pdb2pqr-doc.pdb2pqr
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/doc/
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/doc/pdb2pqr-doc/
-rw-r--r-- root/root      1225 2023-06-12 17:35 ./usr/share/doc/pdb2pqr-doc/changelog.Debian.gz
-rw-r--r-- root/root      5952 2023-06-12 17:29 ./usr/share/doc/pdb2pqr-doc/copyright
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/examples/
drwxr-xr-x root/root         0 2023-03-12 20:52 ./usr/share/doc/pdb2pqr/examples/1a1p/
-rw-r--r-- root/root     16929 2023-03-12 20:52 ./usr/share/doc/pdb2pqr/examples/1a1p/1a1p.pdb
-rw-r--r-- root/root      3481 2023-03-12 20:52 ./usr/share/doc/pdb2pqr/examples/1a1p/README
drwxr-xr-x root/root         0 2023-03-12 20:52 ./usr/share/doc/pdb2pqr/examples/graphcut/
-rwxr-xr-x root/root      1419 2023-03-12 20:52 ./usr/share/doc/pdb2pqr/examples/graphcut/run-graphcut.sh
drwxr-xr-x root/root         0 2023-03-12 20:52 ./usr/share/doc/pdb2pqr/examples/ligands/
-rw-r--r-- root/root      2257 2023-03-12 20:52 ./usr/share/doc/pdb2pqr/examples/ligands/LIG_1ABF.mol2
-rw-r--r-- root/root      7389 2023-03-12 20:52 ./usr/share/doc/pdb2pqr/examples/ligands/LIG_1HPV.mol2
-rw-r--r-- root/root      8035 2023-03-12 20:52 ./usr/share/doc/pdb2pqr/examples/ligands/LIG_1HPX.mol2
-rw-r--r-- root/root      8455 2023-03-12 20:52 ./usr/share/doc/pdb2pqr/examples/ligands/LIG_1QBS.mol2
-rw-r--r-- root/root      8002 2023-03-12 20:52 ./usr/share/doc/pdb2pqr/examples/ligands/LIG_1XL5.mol2
-rw-r--r-- root/root       230 2023-03-12 20:52 ./usr/share/doc/pdb2pqr/examples/ligands/README
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/
-rw-r--r-- root/root      5631 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/index.html
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/
-rw-r--r-- root/root    133993 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/aa.html
-rw-r--r-- root/root    187518 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/biomolecule.html
-rw-r--r-- root/root     18091 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/cells.html
-rw-r--r-- root/root    199717 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/cif.html
-rw-r--r-- root/root     67893 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/debump.html
-rw-r--r-- root/root     54837 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/definitions.html
-rw-r--r-- root/root    143654 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/forcefield.html
-rw-r--r-- root/root    143922 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/hydrogens.html
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/hydrogens/
-rw-r--r-- root/root     93477 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/hydrogens/optimize.html
-rw-r--r-- root/root    222864 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/hydrogens/structures.html
-rw-r--r-- root/root     67051 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/inputgen.html
-rw-r--r-- root/root     89053 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/io.html
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/ligand/
-rw-r--r-- root/root     88032 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/ligand/mol2.html
-rw-r--r-- root/root     32067 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/ligand/peoe.html
-rw-r--r-- root/root      6444 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/ligand/topology.html
-rw-r--r-- root/root    116161 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/main.html
-rw-r--r-- root/root     34765 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/na.html
-rw-r--r-- root/root    352008 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/pdb.html
-rw-r--r-- root/root     85892 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/psize.html
-rw-r--r-- root/root     80896 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/quatfit.html
-rw-r--r-- root/root     49207 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/residue.html
-rw-r--r-- root/root     14243 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/run.html
-rw-r--r-- root/root     57308 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/html/_modules/pdb2pqr/structures.html
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pdb2pqr_3.6.1+dfsg-1_all.deb
----------------------------

 new Debian package, version 2.0.
 size 10430 bytes: control archive=1058 bytes.
    1013 bytes,    21 lines      control              
     631 bytes,    10 lines      md5sums              
 Package: pdb2pqr
 Version: 3.6.1+dfsg-1
 Architecture: all
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 31
 Depends: python3-numpy, python3-pdb2pqr, python3:any
 Suggests: apbs
 Section: science
 Priority: optional
 Homepage: https://www.poissonboltzmann.org
 Description: Preparation of protein structures for electrostatics calculations
  PDB2PQR is a Python software package that automates many of the common
  tasks of preparing structures for continuum electrostatics calculations.
  It thus provides a platform-independent utility for converting protein files
  in PDB format to PQR format. These tasks include:
   * Adding a limited number of missing heavy atoms to biomolecular structures
   * Determining side-chain pKas
   * Placing missing hydrogens
   * Optimizing the protein for favorable hydrogen bonding
   * Assigning charge and radius parameters from a variety of force fields

drwxr-xr-x root/root         0 2023-06-12 17:35 ./
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/bin/
-rwxr-xr-x root/root       958 2023-06-12 17:35 ./usr/bin/dx2cube
-rwxr-xr-x root/root       960 2023-06-12 17:35 ./usr/bin/inputgen
lrwxrwxrwx root/root         0 2023-06-12 17:35 ./usr/bin/pdb2pqr -> pdb2pqr30
-rwxr-xr-x root/root       962 2023-06-12 17:35 ./usr/bin/pdb2pqr30
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/doc/
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/
-rw-r--r-- root/root      1565 2023-06-12 17:29 ./usr/share/doc/pdb2pqr/README.test
lrwxrwxrwx root/root         0 2023-06-12 17:35 ./usr/share/doc/pdb2pqr/changelog.Debian.gz -> ../python3-pdb2pqr/changelog.Debian.gz
-rw-r--r-- root/root      5952 2023-06-12 17:29 ./usr/share/doc/pdb2pqr/copyright
-rw-r--r-- root/root       259 2023-06-12 17:29 ./usr/share/doc/pdb2pqr/installation-test
-rw-r--r-- root/root       655 2023-06-12 17:29 ./usr/share/doc/pdb2pqr/pdb2pka-test
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/man/
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/share/man/man1/
-rw-r--r-- root/root       485 2023-06-12 17:35 ./usr/share/man/man1/dx2cube.1.gz
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lrwxrwxrwx root/root         0 2023-06-12 17:35 ./usr/share/man/man1/pdb2pqr.1.gz -> pdb2pqr30.1.gz
-rw-r--r-- root/root      2645 2023-06-12 17:35 ./usr/share/man/man1/pdb2pqr30.1.gz


python3-pdb2pqr_3.6.1+dfsg-1_all.deb
------------------------------------

 new Debian package, version 2.0.
 size 144652 bytes: control archive=2650 bytes.
    1072 bytes,    21 lines      control              
    4686 bytes,    54 lines      md5sums              
     265 bytes,    12 lines   *  postinst             #!/bin/sh
     378 bytes,    12 lines   *  prerm                #!/bin/sh
 Package: python3-pdb2pqr
 Source: pdb2pqr
 Version: 3.6.1+dfsg-1
 Architecture: all
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1142
 Depends: python3-docutils, python3-numpy, python3-pdbx, python3-propka, python3-requests, python3:any
 Section: python
 Priority: optional
 Homepage: https://www.poissonboltzmann.org
 Description: Preparation of protein structures for electrostatics calculations
  PDB2PQR is a Python software package that automates many of the common
  tasks of preparing structures for continuum electrostatics calculations.
  It thus provides a platform-independent utility for converting protein files
  in PDB format to PQR format. These tasks include:
   * Adding a limited number of missing heavy atoms to biomolecular structures
   * Determining side-chain pKas
   * Placing missing hydrogens
   * Optimizing the protein for favorable hydrogen bonding
   * Assigning charge and radius parameters from a variety of force fields

drwxr-xr-x root/root         0 2023-06-12 17:35 ./
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/lib/
drwxr-xr-x root/root         0 2023-06-12 17:35 ./usr/lib/python3/
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+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not removing build depends: as requested

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: amd64
Build Type: binary
Build-Space: 75016
Build-Time: 91
Distribution: mantic-proposed
Host Architecture: amd64
Install-Time: 27
Job: pdb2pqr_3.6.1+dfsg-1.dsc
Machine Architecture: amd64
Package: pdb2pqr
Package-Time: 119
Source-Version: 3.6.1+dfsg-1
Space: 75016
Status: successful
Version: 3.6.1+dfsg-1
--------------------------------------------------------------------------------
Finished at 2023-06-12T23:17:01Z
Build needed 00:01:59, 75016k disk space
RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26299803
Scanning for processes to kill in build PACKAGEBUILD-26299803