I: pbuilder: network access will be disabled during build
I: Current time: Mon Jul  8 06:53:46 -12 2024
I: pbuilder-time-stamp: 1720464826
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [pdb2pqr_3.5.2+dfsg-3.dsc]
I: copying [./pdb2pqr_3.5.2+dfsg.orig.tar.xz]
I: copying [./pdb2pqr_3.5.2+dfsg-3.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sat Feb  4 20:07:43 2023 -12
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.5.2+dfsg-3.dsc: no acceptable signature found
dpkg-source: info: extracting pdb2pqr in pdb2pqr-3.5.2+dfsg
dpkg-source: info: unpacking pdb2pqr_3.5.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking pdb2pqr_3.5.2+dfsg-3.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
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/49292/tmp/hooks/D02_print_environment starting
I: set
  BUILDDIR='/build'
  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
  BUILDUSERNAME='pbuilder1'
  BUILD_ARCH='i386'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 '
  DISTRIBUTION='bookworm'
  HOME='/root'
  HOST_ARCH='i386'
  IFS=' 	
  '
  INVOCATION_ID='bae00b8c1ed04dba82d4fa99cc745bde'
  LANG='C'
  LANGUAGE='en_US:en'
  LC_ALL='C'
  LD_LIBRARY_PATH='/usr/lib/libeatmydata'
  LD_PRELOAD='libeatmydata.so'
  MAIL='/var/mail/root'
  OPTIND='1'
  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
  PBCURRENTCOMMANDLINEOPERATION='build'
  PBUILDER_OPERATION='build'
  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
  PBUILDER_SYSCONFDIR='/etc'
  PPID='49292'
  PS1='# '
  PS2='> '
  PS4='+ '
  PWD='/'
  SHELL='/bin/bash'
  SHLVL='2'
  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.bKBR9kUt/pbuilderrc_uiII --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bKBR9kUt/b1 --logfile b1/build.log pdb2pqr_3.5.2+dfsg-3.dsc'
  SUDO_GID='112'
  SUDO_UID='107'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT+12'
  USER='root'
  _='/usr/bin/systemd-run'
  http_proxy='http://85.184.249.68:3128'
I: uname -a
  Linux ionos6-i386 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux
I: ls -l /bin
  total 6036
  -rwxr-xr-x 1 root root 1408088 Apr 23  2023 bash
  -rwxr-xr-x 3 root root   38404 Sep 18  2022 bunzip2
  -rwxr-xr-x 3 root root   38404 Sep 18  2022 bzcat
  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzcmp -> bzdiff
  -rwxr-xr-x 1 root root    2225 Sep 18  2022 bzdiff
  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzegrep -> bzgrep
  -rwxr-xr-x 1 root root    4893 Nov 27  2021 bzexe
  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzfgrep -> bzgrep
  -rwxr-xr-x 1 root root    3775 Sep 18  2022 bzgrep
  -rwxr-xr-x 3 root root   38404 Sep 18  2022 bzip2
  -rwxr-xr-x 1 root root   17892 Sep 18  2022 bzip2recover
  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzless -> bzmore
  -rwxr-xr-x 1 root root    1297 Sep 18  2022 bzmore
  -rwxr-xr-x 1 root root   42920 Sep 20  2022 cat
  -rwxr-xr-x 1 root root   79816 Sep 20  2022 chgrp
  -rwxr-xr-x 1 root root   67496 Sep 20  2022 chmod
  -rwxr-xr-x 1 root root   79816 Sep 20  2022 chown
  -rwxr-xr-x 1 root root  162024 Sep 20  2022 cp
  -rwxr-xr-x 1 root root  136916 Jan  5  2023 dash
  -rwxr-xr-x 1 root root  137160 Sep 20  2022 date
  -rwxr-xr-x 1 root root  100364 Sep 20  2022 dd
  -rwxr-xr-x 1 root root  108940 Sep 20  2022 df
  -rwxr-xr-x 1 root root  162152 Sep 20  2022 dir
  -rwxr-xr-x 1 root root   87760 Mar 22  2023 dmesg
  lrwxrwxrwx 1 root root       8 Dec 19  2022 dnsdomainname -> hostname
  lrwxrwxrwx 1 root root       8 Dec 19  2022 domainname -> hostname
  -rwxr-xr-x 1 root root   38760 Sep 20  2022 echo
  -rwxr-xr-x 1 root root      41 Jan 24  2023 egrep
  -rwxr-xr-x 1 root root   34664 Sep 20  2022 false
  -rwxr-xr-x 1 root root      41 Jan 24  2023 fgrep
  -rwxr-xr-x 1 root root   84272 Mar 22  2023 findmnt
  -rwsr-xr-x 1 root root   30240 Mar 22  2023 fusermount
  -rwxr-xr-x 1 root root  218680 Jan 24  2023 grep
  -rwxr-xr-x 2 root root    2346 Apr  9  2022 gunzip
  -rwxr-xr-x 1 root root    6447 Apr  9  2022 gzexe
  -rwxr-xr-x 1 root root  100952 Apr  9  2022 gzip
  -rwxr-xr-x 1 root root   21916 Dec 19  2022 hostname
  -rwxr-xr-x 1 root root   75756 Sep 20  2022 ln
  -rwxr-xr-x 1 root root   55600 Mar 22  2023 login
  -rwxr-xr-x 1 root root  162152 Sep 20  2022 ls
  -rwxr-xr-x 1 root root  214568 Mar 22  2023 lsblk
  -rwxr-xr-x 1 root root   96328 Sep 20  2022 mkdir
  -rwxr-xr-x 1 root root   84008 Sep 20  2022 mknod
  -rwxr-xr-x 1 root root   38792 Sep 20  2022 mktemp
  -rwxr-xr-x 1 root root   63016 Mar 22  2023 more
  -rwsr-xr-x 1 root root   58912 Mar 22  2023 mount
  -rwxr-xr-x 1 root root   13856 Mar 22  2023 mountpoint
  -rwxr-xr-x 1 root root  157932 Sep 20  2022 mv
  lrwxrwxrwx 1 root root       8 Dec 19  2022 nisdomainname -> hostname
  lrwxrwxrwx 1 root root      14 Apr  2  2023 pidof -> /sbin/killall5
  -rwxr-xr-x 1 root root   38792 Sep 20  2022 pwd
  lrwxrwxrwx 1 root root       4 Apr 23  2023 rbash -> bash
  -rwxr-xr-x 1 root root   51080 Sep 20  2022 readlink
  -rwxr-xr-x 1 root root   75720 Sep 20  2022 rm
  -rwxr-xr-x 1 root root   51080 Sep 20  2022 rmdir
  -rwxr-xr-x 1 root root   22308 Nov  2  2022 run-parts
  -rwxr-xr-x 1 root root  133224 Jan  5  2023 sed
  lrwxrwxrwx 1 root root       4 Jan  5  2023 sh -> dash
  -rwxr-xr-x 1 root root   38760 Sep 20  2022 sleep
  -rwxr-xr-x 1 root root   87976 Sep 20  2022 stty
  -rwsr-xr-x 1 root root   83492 Mar 22  2023 su
  -rwxr-xr-x 1 root root   38792 Sep 20  2022 sync
  -rwxr-xr-x 1 root root  598456 Apr  6  2023 tar
  -rwxr-xr-x 1 root root   13860 Nov  2  2022 tempfile
  -rwxr-xr-x 1 root root  120776 Sep 20  2022 touch
  -rwxr-xr-x 1 root root   34664 Sep 20  2022 true
  -rwxr-xr-x 1 root root   17892 Mar 22  2023 ulockmgr_server
  -rwsr-xr-x 1 root root   30236 Mar 22  2023 umount
  -rwxr-xr-x 1 root root   38760 Sep 20  2022 uname
  -rwxr-xr-x 2 root root    2346 Apr  9  2022 uncompress
  -rwxr-xr-x 1 root root  162152 Sep 20  2022 vdir
  -rwxr-xr-x 1 root root   71216 Mar 22  2023 wdctl
  lrwxrwxrwx 1 root root       8 Dec 19  2022 ypdomainname -> hostname
  -rwxr-xr-x 1 root root    1984 Apr  9  2022 zcat
  -rwxr-xr-x 1 root root    1678 Apr  9  2022 zcmp
  -rwxr-xr-x 1 root root    6460 Apr  9  2022 zdiff
  -rwxr-xr-x 1 root root      29 Apr  9  2022 zegrep
  -rwxr-xr-x 1 root root      29 Apr  9  2022 zfgrep
  -rwxr-xr-x 1 root root    2081 Apr  9  2022 zforce
  -rwxr-xr-x 1 root root    8103 Apr  9  2022 zgrep
  -rwxr-xr-x 1 root root    2206 Apr  9  2022 zless
  -rwxr-xr-x 1 root root    1842 Apr  9  2022 zmore
  -rwxr-xr-x 1 root root    4577 Apr  9  2022 znew
I: user script /srv/workspace/pbuilder/49292/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), dh-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
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19599 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on dh-python; however:
  Package dh-python is not installed.
 pbuilder-satisfydepends-dummy depends on dh-sequence-sphinxdoc; however:
  Package dh-sequence-sphinxdoc is not installed.
 pbuilder-satisfydepends-dummy depends on help2man; however:
  Package help2man is not installed.
 pbuilder-satisfydepends-dummy depends on python3-dev; however:
  Package python3-dev is not installed.
 pbuilder-satisfydepends-dummy depends on python3-numpy; however:
  Package python3-numpy is not installed.
 pbuilder-satisfydepends-dummy depends on python3-pdbx; however:
  Package python3-pdbx is not installed.
 pbuilder-satisfydepends-dummy depends on python3-pandas; however:
  Package python3-pandas is not installed.
 pbuilder-satisfydepends-dummy depends on python3-propka; however:
  Package python3-propka is not installed.
 pbuilder-satisfydepends-dummy depends on python3-pytest; however:
  Package python3-pytest is not installed.
 pbuilder-satisfydepends-dummy depends on python3-setuptools; however:
  Package python3-setuptools is not installed.
 pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however:
  Package python3-sphinx-rtd-theme is not installed.
 pbuilder-satisfydepends-dummy depends on python3-testfixtures; however:
  Package python3-testfixtures is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-font-awesome{a} fonts-lato{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} openssl{a} po-debconf{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-attr{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-dateutil{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-iniconfig{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pdbx{a} python3-pkg-resources{a} python3-pluggy{a} python3-propka{a} python3-py{a} python3-pygments{a} python3-pytest{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-testfixtures{a} python3-tz{a} python3-urllib3{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} xml-core{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  curl javascript-common libarchive-cpio-perl libjson-xs-perl libltdl-dev libmail-sendmail-perl libpaper-utils lynx python3-bottleneck python3-bs4 python3-html5lib python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pil python3-scipy python3-tables wget 
0 packages upgraded, 105 newly installed, 0 to remove and 0 not upgraded.
Need to get 66.3 MB of archives. After unpacking 286 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 fonts-lato all 2.0-2.1 [2696 kB]
Get: 2 http://deb.debian.org/debian bookworm/main i386 liblocale-gettext-perl i386 1.07-5 [15.5 kB]
Get: 3 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB]
Get: 11 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B]
Get: 13 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 sgml-base all 1.31 [15.4 kB]
Get: 15 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 openssl i386 3.0.9-1 [1420 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 ca-certificates all 20230311 [153 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 21 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 22 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 23 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 24 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 26 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 31 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 32 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 33 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 34 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 35 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 36 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 37 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 38 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 39 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 40 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 41 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 42 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB]
Get: 43 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 44 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 45 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 46 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Get: 47 http://deb.debian.org/debian bookworm/main i386 python3-lib2to3 all 3.11.2-3 [76.3 kB]
Get: 48 http://deb.debian.org/debian bookworm/main i386 python3-distutils all 3.11.2-3 [131 kB]
Get: 49 http://deb.debian.org/debian bookworm/main i386 dh-python all 5.20230130 [104 kB]
Get: 50 http://deb.debian.org/debian bookworm/main i386 xml-core all 0.18+nmu1 [23.8 kB]
Get: 51 http://deb.debian.org/debian bookworm/main i386 docutils-common all 0.19+dfsg-6 [127 kB]
Get: 52 http://deb.debian.org/debian bookworm/main i386 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB]
Get: 53 http://deb.debian.org/debian bookworm/main i386 help2man i386 1.49.3 [198 kB]
Get: 54 http://deb.debian.org/debian bookworm/main i386 libblas3 i386 3.11.0-2 [139 kB]
Get: 55 http://deb.debian.org/debian bookworm/main i386 libexpat1-dev i386 2.5.0-1 [158 kB]
Get: 56 http://deb.debian.org/debian bookworm/main i386 libgfortran5 i386 12.2.0-14 [698 kB]
Get: 57 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 58 http://deb.debian.org/debian bookworm/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 59 http://deb.debian.org/debian bookworm/main i386 libjs-sphinxdoc all 5.3.0-4 [130 kB]
Get: 60 http://deb.debian.org/debian bookworm/main i386 libjson-perl all 4.10000-1 [87.5 kB]
Get: 61 http://deb.debian.org/debian bookworm/main i386 liblapack3 i386 3.11.0-2 [2092 kB]
Get: 62 http://deb.debian.org/debian bookworm/main i386 libpython3.11 i386 3.11.2-6 [2013 kB]
Get: 63 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB]
Get: 64 http://deb.debian.org/debian bookworm/main i386 libpython3.11-dev i386 3.11.2-6 [4906 kB]
Get: 65 http://deb.debian.org/debian bookworm/main i386 libpython3-dev i386 3.11.2-1+b1 [9580 B]
Get: 66 http://deb.debian.org/debian bookworm/main i386 python-babel-localedata all 2.10.3-1 [5615 kB]
Get: 67 http://deb.debian.org/debian bookworm/main i386 python3-alabaster all 0.7.12-1 [20.8 kB]
Get: 68 http://deb.debian.org/debian bookworm/main i386 python3-attr all 22.2.0-1 [65.4 kB]
Get: 69 http://deb.debian.org/debian bookworm/main i386 python3-pkg-resources all 66.1.1-1 [296 kB]
Get: 70 http://deb.debian.org/debian bookworm/main i386 python3-tz all 2022.7.1-4 [30.1 kB]
Get: 71 http://deb.debian.org/debian bookworm/main i386 python3-babel all 2.10.3-1 [103 kB]
Get: 72 http://deb.debian.org/debian bookworm/main i386 python3-certifi all 2022.9.24-1 [153 kB]
Get: 73 http://deb.debian.org/debian bookworm/main i386 python3-chardet all 5.1.0+dfsg-2 [110 kB]
Get: 74 http://deb.debian.org/debian bookworm/main i386 python3-charset-normalizer all 3.0.1-2 [49.3 kB]
Get: 75 http://deb.debian.org/debian bookworm/main i386 python3-six all 1.16.0-4 [17.5 kB]
Get: 76 http://deb.debian.org/debian bookworm/main i386 python3-dateutil all 2.8.2-2 [78.3 kB]
Get: 77 http://deb.debian.org/debian bookworm/main i386 python3.11-dev i386 3.11.2-6 [615 kB]
Get: 78 http://deb.debian.org/debian bookworm/main i386 python3-dev i386 3.11.2-1+b1 [26.2 kB]
Get: 79 http://deb.debian.org/debian bookworm/main i386 python3-roman all 3.3-3 [9880 B]
Get: 80 http://deb.debian.org/debian bookworm/main i386 python3-docutils all 0.19+dfsg-6 [382 kB]
Get: 81 http://deb.debian.org/debian bookworm/main i386 python3-idna all 3.3-1 [39.4 kB]
Get: 82 http://deb.debian.org/debian bookworm/main i386 python3-imagesize all 1.4.1-1 [6688 B]
Get: 83 http://deb.debian.org/debian bookworm/main i386 python3-iniconfig all 1.1.1-2 [6396 B]
Get: 84 http://deb.debian.org/debian bookworm/main i386 python3-markupsafe i386 2.1.2-1+b1 [13.3 kB]
Get: 85 http://deb.debian.org/debian bookworm/main i386 python3-jinja2 all 3.1.2-1 [119 kB]
Get: 86 http://deb.debian.org/debian bookworm/main i386 python3-more-itertools all 8.10.0-2 [53.0 kB]
Get: 87 http://deb.debian.org/debian bookworm/main i386 python3-numpy i386 1:1.24.2-1 [6115 kB]
Get: 88 http://deb.debian.org/debian bookworm/main i386 python3-packaging all 23.0-1 [32.5 kB]
Get: 89 http://deb.debian.org/debian bookworm/main i386 python3-pandas-lib i386 1.5.3+dfsg-2 [3382 kB]
Get: 90 http://deb.debian.org/debian bookworm/main i386 python3-pandas all 1.5.3+dfsg-2 [2885 kB]
Get: 91 http://deb.debian.org/debian bookworm/main i386 python3-pdbx all 2.0.1-2 [17.4 kB]
Get: 92 http://deb.debian.org/debian bookworm/main i386 python3-pluggy all 1.0.0+repack-1 [19.7 kB]
Get: 93 http://deb.debian.org/debian bookworm/main i386 python3-propka all 3.5.0-1 [65.6 kB]
Get: 94 http://deb.debian.org/debian bookworm/main i386 python3-py all 1.11.0-1 [89.2 kB]
Get: 95 http://deb.debian.org/debian bookworm/main i386 python3-pygments all 2.14.0+dfsg-1 [783 kB]
Get: 96 http://deb.debian.org/debian bookworm/main i386 python3-pytest all 7.2.1-2 [236 kB]
Get: 97 http://deb.debian.org/debian bookworm/main i386 python3-urllib3 all 1.26.12-1 [117 kB]
Get: 98 http://deb.debian.org/debian bookworm/main i386 python3-requests all 2.28.1+dfsg-1 [67.9 kB]
Get: 99 http://deb.debian.org/debian bookworm/main i386 python3-setuptools all 66.1.1-1 [521 kB]
Get: 100 http://deb.debian.org/debian bookworm/main i386 python3-snowballstemmer all 2.2.0-2 [57.8 kB]
Get: 101 http://deb.debian.org/debian bookworm/main i386 sphinx-common all 5.3.0-4 [653 kB]
Get: 102 http://deb.debian.org/debian bookworm/main i386 python3-sphinx all 5.3.0-4 [549 kB]
Get: 103 http://deb.debian.org/debian bookworm/main i386 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB]
Get: 104 http://deb.debian.org/debian bookworm/main i386 python3-sphinx-rtd-theme all 1.2.0+dfsg-1 [27.7 kB]
Get: 105 http://deb.debian.org/debian bookworm/main i386 python3-testfixtures all 7.0.4-1 [79.8 kB]
Fetched 66.3 MB in 1s (95.4 MB/s)
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 -> Finished parsing the build-deps
I: Building the package
I: Running cd /build/pdb2pqr-3.5.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../pdb2pqr_3.5.2+dfsg-3_source.changes
dpkg-buildpackage: info: source package pdb2pqr
dpkg-buildpackage: info: source version 3.5.2+dfsg-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
 debian/rules clean
dh clean --buildsystem pybuild --with python3
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/pdb2pqr-3.5.2+dfsg'
dh_auto_clean
I: pybuild base:240: python3.11 setup.py clean 
running clean
removing '/build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build' (and everything under it)
'build/bdist.linux-i386' 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 '/build/pdb2pqr-3.5.2+dfsg'
   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:240: python3.11 setup.py config 
running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/pdb2pqr-3.5.2+dfsg'
dh_auto_build
I: pybuild base:240: /usr/bin/python3 setup.py build 
running build
running build_py
creating /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/run.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/inputgen.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/aa.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/debump.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/definitions.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/main.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/topology.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/psize.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/cif.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/_version.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/forcefield.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/na.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/__main__.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/structures.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/cells.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/residue.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/config.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/biomolecule.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/utilities.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/pdb.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/io.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
copying pdb2pqr/quatfit.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr
creating /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand
copying pdb2pqr/ligand/topology.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand
copying pdb2pqr/ligand/peoe.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand
copying pdb2pqr/ligand/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand
copying pdb2pqr/ligand/mol2.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand
creating /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens
copying pdb2pqr/hydrogens/structures.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens
copying pdb2pqr/hydrogens/optimize.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens
copying pdb2pqr/hydrogens/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens
creating /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/TOPOLOGY.xml -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/AA.xml -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/NA.xml -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/PATCHES.xml -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/HYDROGENS.xml -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/SWANSON.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/TYL06.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/PARSE.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/PEOEPB.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/AMBER.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/CHARMM.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/AMBER.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/CHARMM.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/SWANSON.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/TYL06.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/PEOEPB.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
copying pdb2pqr/dat/PARSE.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat
PYTHONPATH=. python3 -m sphinx -N -bhtml docs/source build/html
Running Sphinx v5.3.0
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 0xf3f0b210>: 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
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build succeeded, 2 warnings.

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make[1]: Leaving directory '/build/pdb2pqr-3.5.2+dfsg'
   dh_auto_test -O--buildsystem=pybuild
I: pybuild base:240: cd /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build; python3.11 -m pytest tests
============================= test session starts ==============================
platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack
rootdir: /build/pdb2pqr-3.5.2+dfsg, configfile: pytest.ini

----------------------------- live log collection ------------------------------
WARNING  py.warnings:warnings.py:109 /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/tests/core_test.py:80: 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
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tests/core_test.py::test_broken_backbone[4MGP] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_broken_backbone_4MGP_0/4MGP.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: 4MGP
XFAIL                                                                    [ 68%]
tests/core_test.py::test_broken_backbone[2V75] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_broken_backbone_2V75_0/2V75.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: 2V75
XFAIL                                                                    [ 68%]
tests/core_test.py::test_broken_backbone[1EJG] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_broken_backbone_1EJG_0/1EJG.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: 1EJG
XFAIL                                                                    [ 69%]
tests/core_test.py::test_broken_backbone[3U7T] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_broken_backbone_3U7T_0/3U7T.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: 3U7T
XFAIL                                                                    [ 69%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 69%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 70%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 70%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 70%]
tests/io_test.py::test_read_pqr[tests/data/1HPX_with-ph=7.00_titration_state_method=propka_ligand=LIG_1HPX_ff=AMBER.pqr] PASSED [ 71%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED     [ 71%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 71%]
tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED           [ 71%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 72%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 72%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 72%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 73%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 73%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 73%]
tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 74%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 74%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 74%]
tests/io_test.py::test_read_qcd PASSED                                   [ 75%]
tests/io_test.py::test_dx2cube 
-------------------------------- live log call ---------------------------------
INFO     io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr...
INFO     io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx...
INFO     io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-pbuilder1/pytest-0/test_dx2cube0/test.cube...
INFO     io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-pbuilder1/pytest-0/test_dx2cube0/test.cube...
INFO     io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube...
INFO     io_test:io_test.py:68 No differences found in output
PASSED                                                                   [ 75%]
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                                                                   [ 76%]
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                                                                   [ 76%]
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                                                                   [ 76%]
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                                                                   [ 77%]
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                                                                   [ 77%]
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                                                                   [ 77%]
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                                                                   [ 78%]
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                                                                   [ 78%]
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                                                                   [ 78%]
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                                                                   [ 79%]
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                                                                   [ 79%]
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                                                                   [ 79%]
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                                                                   [ 80%]
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                                                                   [ 80%]
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                                                                   [ 80%]
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                                                                   [ 81%]
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                                                                   [ 81%]
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                                                                   [ 81%]
tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED            [ 82%]
tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED       [ 82%]
tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type.
PASSED                                                                   [ 82%]
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                                                                   [ 83%]
tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED         [ 83%]
tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED        [ 83%]
tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED            [ 84%]
tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED         [ 84%]
tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED           [ 84%]
tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED        [ 85%]
tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED            [ 85%]
tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type.
PASSED                                                                   [ 85%]
tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED           [ 85%]
tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED                 [ 86%]
tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED                 [ 86%]
tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED     [ 86%]
tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED                [ 87%]
tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED             [ 87%]
tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED                [ 87%]
tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED                [ 88%]
tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED                [ 88%]
tests/ligand_test.py::test_rings[acetate.mol2] PASSED                    [ 88%]
tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED               [ 89%]
tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED              [ 89%]
tests/ligand_test.py::test_rings[adp.mol2] PASSED                        [ 89%]
tests/ligand_test.py::test_rings[anthracene.mol2] PASSED                 [ 90%]
tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED                [ 90%]
tests/ligand_test.py::test_rings[ethanol.mol2] PASSED                    [ 90%]
tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED                 [ 91%]
tests/ligand_test.py::test_rings[glycerol.mol2] PASSED                   [ 91%]
tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED                [ 91%]
tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED                    [ 92%]
tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED        [ 92%]
tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 92%]
tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 93%]
tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 93%]
tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 93%]
tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 94%]
tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 94%]
tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 94%]
tests/regression_test.py::test_basic[1AFS basic local] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_basic_1AFS_basic_local_0/output.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.5.2:main.py:763 Setting up molecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:966 Unable to find amino or nucleic acid definition for NAP.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:966 Unable to find amino or nucleic acid definition for TES.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:966 Unable to find amino or nucleic acid definition for NAP.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:966 Unable to find amino or nucleic acid definition for TES.  Parsing as new residue.
INFO     PDB2PQR3.5.2:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.5.2:main.py:767 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.5.2:main.py:603 Loading forcefield.
INFO     PDB2PQR3.5.2:main.py:607 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     PDB2PQR3.5.2:main.py:617 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:1051 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1051 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.5.2:main.py:622 Updating disulfide bridges.
INFO     PDB2PQR3.5.2:main.py:625 Debumping biomolecule.
INFO     PDB2PQR3.5.2:main.py:642 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.5.2:main.py:645 Debumping biomolecule (again).
INFO     PDB2PQR3.5.2:main.py:647 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     PDB2PQR3.5.2:main.py:659 Applying force field to biomolecule states.
INFO     PDB2PQR3.5.2:main.py:706 Regenerating headers.
INFO     PDB2PQR3.5.2:main.py:731 Regenerating PDB lines.
WARNING  PDB2PQR3.5.2:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.5.2:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:179 6 atoms have position differences > 0
INFO     common:common.py:191 0 atoms have position differences > 0.01
INFO     common:common.py:191 0 atoms have charge differences > 0
INFO     common:common.py:191 0 atoms have charge differences > 0.01
INFO     common:common.py:191 0 atoms have radius differences > 0
INFO     common:common.py:191 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-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa0/output.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.5.2:main.py:763 Setting up molecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:966 Unable to find amino or nucleic acid definition for NAP.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:966 Unable to find amino or nucleic acid definition for TES.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:966 Unable to find amino or nucleic acid definition for NAP.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:966 Unable to find amino or nucleic acid definition for TES.  Parsing as new residue.
INFO     PDB2PQR3.5.2:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.5.2:main.py:767 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.5.2:main.py:603 Loading forcefield.
INFO     PDB2PQR3.5.2:main.py:607 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     PDB2PQR3.5.2:main.py:617 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:1051 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1051 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.5.2:main.py:622 Updating disulfide bridges.
INFO     PDB2PQR3.5.2:main.py:625 Debumping biomolecule.
INFO     PDB2PQR3.5.2:main.py:642 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.5.2:main.py:645 Debumping biomolecule (again).
INFO     PDB2PQR3.5.2:main.py:647 Optimizing hydrogen bonds
INFO     PDB2PQR3.5.2:main.py:659 Applying force field to biomolecule states.
INFO     PDB2PQR3.5.2:main.py:706 Regenerating headers.
INFO     PDB2PQR3.5.2:main.py:731 Regenerating PDB lines.
WARNING  PDB2PQR3.5.2:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.5.2:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:179 6 atoms have position differences > 0
INFO     common:common.py:191 0 atoms have position differences > 0.01
INFO     common:common.py:191 0 atoms have charge differences > 0
INFO     common:common.py:191 0 atoms have charge differences > 0.01
INFO     common:common.py:191 0 atoms have radius differences > 0
INFO     common:common.py:191 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-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa1/output.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.5.2:main.py:763 Setting up molecule.
WARNING  pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages
INFO     PDB2PQR3.5.2:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.5.2:main.py:767 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.5.2:main.py:603 Loading forcefield.
INFO     PDB2PQR3.5.2:main.py:607 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     PDB2PQR3.5.2:main.py:617 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:1051 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1051 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.5.2:main.py:622 Updating disulfide bridges.
INFO     PDB2PQR3.5.2:main.py:625 Debumping biomolecule.
INFO     PDB2PQR3.5.2:main.py:642 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.5.2:main.py:645 Debumping biomolecule (again).
INFO     PDB2PQR3.5.2:main.py:647 Optimizing hydrogen bonds
INFO     PDB2PQR3.5.2:main.py:659 Applying force field to biomolecule states.
INFO     PDB2PQR3.5.2:main.py:706 Regenerating headers.
INFO     PDB2PQR3.5.2:main.py:731 Regenerating PDB lines.
WARNING  PDB2PQR3.5.2:main.py:311 Ignoring 5426 header lines in output.
WARNING  PDB2PQR3.5.2:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:179 5 atoms have position differences > 0
INFO     common:common.py:191 0 atoms have position differences > 0.01
INFO     common:common.py:191 0 atoms have charge differences > 0
INFO     common:common.py:191 0 atoms have charge differences > 0.01
INFO     common:common.py:191 0 atoms have radius differences > 0
INFO     common:common.py:191 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-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa2/output.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.5.2:main.py:763 Setting up molecule.
INFO     PDB2PQR3.5.2:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.5.2:main.py:767 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.5.2:main.py:603 Loading forcefield.
INFO     PDB2PQR3.5.2:main.py:607 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     PDB2PQR3.5.2:main.py:617 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:1051 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1051 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.5.2:main.py:622 Updating disulfide bridges.
INFO     PDB2PQR3.5.2:main.py:625 Debumping biomolecule.
INFO     PDB2PQR3.5.2:main.py:642 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.5.2:main.py:645 Debumping biomolecule (again).
INFO     PDB2PQR3.5.2:main.py:647 Optimizing hydrogen bonds
INFO     PDB2PQR3.5.2:main.py:659 Applying force field to biomolecule states.
INFO     PDB2PQR3.5.2:main.py:706 Regenerating headers.
INFO     PDB2PQR3.5.2:main.py:731 Regenerating PDB lines.
WARNING  PDB2PQR3.5.2:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.5.2:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:179 6 atoms have position differences > 0
INFO     common:common.py:191 0 atoms have position differences > 0.01
INFO     common:common.py:191 0 atoms have charge differences > 0
INFO     common:common.py:191 0 atoms have charge differences > 0.01
INFO     common:common.py:191 0 atoms have radius differences > 0
INFO     common:common.py:191 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-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa3/output.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.5.2:main.py:763 Setting up molecule.
INFO     PDB2PQR3.5.2:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.5.2:main.py:767 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.5.2:main.py:603 Loading forcefield.
INFO     PDB2PQR3.5.2:main.py:607 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     PDB2PQR3.5.2:main.py:617 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:1051 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1051 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.5.2:main.py:622 Updating disulfide bridges.
INFO     PDB2PQR3.5.2:main.py:625 Debumping biomolecule.
INFO     PDB2PQR3.5.2:main.py:642 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.5.2:main.py:645 Debumping biomolecule (again).
INFO     PDB2PQR3.5.2:main.py:647 Optimizing hydrogen bonds
INFO     PDB2PQR3.5.2:main.py:659 Applying force field to biomolecule states.
INFO     PDB2PQR3.5.2:main.py:706 Regenerating headers.
INFO     PDB2PQR3.5.2:main.py:731 Regenerating PDB lines.
WARNING  PDB2PQR3.5.2:main.py:311 Ignoring 5426 header lines in output.
WARNING  PDB2PQR3.5.2:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:179 6 atoms have position differences > 0
INFO     common:common.py:191 0 atoms have position differences > 0.01
INFO     common:common.py:191 0 atoms have charge differences > 0
INFO     common:common.py:191 0 atoms have charge differences > 0.01
INFO     common:common.py:191 0 atoms have radius differences > 0
INFO     common:common.py:191 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-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa4/output.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.5.2:main.py:763 Setting up molecule.
INFO     PDB2PQR3.5.2:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.5.2:main.py:767 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.5.2:main.py:603 Loading forcefield.
INFO     PDB2PQR3.5.2:main.py:607 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     PDB2PQR3.5.2:main.py:617 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:1051 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1051 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.5.2:main.py:622 Updating disulfide bridges.
INFO     PDB2PQR3.5.2:main.py:625 Debumping biomolecule.
INFO     PDB2PQR3.5.2:main.py:642 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.5.2:main.py:645 Debumping biomolecule (again).
INFO     PDB2PQR3.5.2:main.py:647 Optimizing hydrogen bonds
INFO     PDB2PQR3.5.2:main.py:659 Applying force field to biomolecule states.
INFO     PDB2PQR3.5.2:main.py:706 Regenerating headers.
INFO     PDB2PQR3.5.2:main.py:731 Regenerating PDB lines.
WARNING  PDB2PQR3.5.2:main.py:311 Ignoring 5428 header lines in output.
WARNING  PDB2PQR3.5.2:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:179 6 atoms have position differences > 0
INFO     common:common.py:191 0 atoms have position differences > 0.01
INFO     common:common.py:191 0 atoms have charge differences > 0
INFO     common:common.py:191 0 atoms have charge differences > 0.01
INFO     common:common.py:191 0 atoms have radius differences > 0
INFO     common:common.py:191 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-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa5/output.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.5.2:main.py:763 Setting up molecule.
INFO     PDB2PQR3.5.2:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.5.2:main.py:767 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.5.2:main.py:603 Loading forcefield.
INFO     PDB2PQR3.5.2:main.py:607 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     PDB2PQR3.5.2:main.py:617 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:1051 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1051 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.5.2:main.py:622 Updating disulfide bridges.
INFO     PDB2PQR3.5.2:main.py:625 Debumping biomolecule.
INFO     PDB2PQR3.5.2:main.py:642 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.5.2:main.py:645 Debumping biomolecule (again).
INFO     PDB2PQR3.5.2:main.py:647 Optimizing hydrogen bonds
INFO     PDB2PQR3.5.2:main.py:659 Applying force field to biomolecule states.
INFO     PDB2PQR3.5.2:main.py:706 Regenerating headers.
INFO     PDB2PQR3.5.2:main.py:731 Regenerating PDB lines.
WARNING  PDB2PQR3.5.2:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.5.2:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:179 6 atoms have position differences > 0
INFO     common:common.py:191 0 atoms have position differences > 0.01
INFO     common:common.py:191 0 atoms have charge differences > 0
INFO     common:common.py:191 0 atoms have charge differences > 0.01
INFO     common:common.py:191 0 atoms have radius differences > 0
INFO     common:common.py:191 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-pbuilder1/pytest-0/test_other_options_1AFS_whites0/output.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.5.2:main.py:763 Setting up molecule.
INFO     PDB2PQR3.5.2:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.5.2:main.py:767 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.5.2:main.py:771 Arguments specified cleaning only; skipping remaining steps.
INFO     common:common.py:191 0 atoms have position differences > 0
INFO     common:common.py:191 0 atoms have position differences > 0.01
INFO     common:common.py:191 0 atoms have charge differences > 0
INFO     common:common.py:191 0 atoms have charge differences > 0.01
INFO     common:common.py:191 0 atoms have radius differences > 0
INFO     common:common.py:191 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-pbuilder1/pytest-0/test_other_options_1A1P_assign0/output.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: tests/data/1A1P.pdb
INFO     PDB2PQR3.5.2:main.py:763 Setting up molecule.
INFO     PDB2PQR3.5.2:main.py:408 Created biomolecule object with 14 residues and 208 atoms.
INFO     PDB2PQR3.5.2:main.py:767 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.5.2:main.py:603 Loading forcefield.
INFO     PDB2PQR3.5.2:main.py:607 Loading hydrogen topology definitions.
INFO     PDB2PQR3.5.2:main.py:659 Applying force field to biomolecule states.
INFO     PDB2PQR3.5.2:main.py:706 Regenerating headers.
INFO     PDB2PQR3.5.2:main.py:731 Regenerating PDB lines.
WARNING  PDB2PQR3.5.2:main.py:311 Ignoring 852 header lines in output.
WARNING  PDB2PQR3.5.2:main.py:315 Ignoring 3 missing lines in output.
INFO     common:common.py:191 0 atoms have position differences > 0
INFO     common:common.py:191 0 atoms have position differences > 0.01
INFO     common:common.py:191 0 atoms have charge differences > 0
INFO     common:common.py:191 0 atoms have charge differences > 0.01
INFO     common:common.py:191 0 atoms have radius differences > 0
INFO     common:common.py:191 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-pbuilder1/pytest-0/test_other_options_1A1P_nodebu0/output.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: tests/data/1A1P.pdb
INFO     PDB2PQR3.5.2:main.py:763 Setting up molecule.
INFO     PDB2PQR3.5.2:main.py:408 Created biomolecule object with 14 residues and 208 atoms.
INFO     PDB2PQR3.5.2:main.py:767 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.5.2:main.py:603 Loading forcefield.
INFO     PDB2PQR3.5.2:main.py:607 Loading hydrogen topology definitions.
INFO     PDB2PQR3.5.2:main.py:459 This biomolecule is clean.  No repair needed.
INFO     PDB2PQR3.5.2:main.py:622 Updating disulfide bridges.
INFO     PDB2PQR3.5.2:main.py:642 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.5.2:main.py:647 Optimizing hydrogen bonds
INFO     pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization...
INFO     PDB2PQR3.5.2:main.py:659 Applying force field to biomolecule states.
INFO     PDB2PQR3.5.2:main.py:706 Regenerating headers.
INFO     PDB2PQR3.5.2:main.py:731 Regenerating PDB lines.
WARNING  PDB2PQR3.5.2:main.py:311 Ignoring 852 header lines in output.
WARNING  PDB2PQR3.5.2:main.py:315 Ignoring 3 missing lines in output.
INFO     common:common.py:191 0 atoms have position differences > 0
INFO     common:common.py:191 0 atoms have position differences > 0.01
INFO     common:common.py:191 0 atoms have charge differences > 0
INFO     common:common.py:191 0 atoms have charge differences > 0.01
INFO     common:common.py:191 0 atoms have radius differences > 0
INFO     common:common.py:191 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-pbuilder1/pytest-0/test_other_options_1AFS_chain_0/output.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.5.2:main.py:763 Setting up molecule.
INFO     PDB2PQR3.5.2:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.5.2:main.py:767 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.5.2:main.py:603 Loading forcefield.
INFO     PDB2PQR3.5.2:main.py:607 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     PDB2PQR3.5.2:main.py:617 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:1051 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1051 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.5.2:main.py:622 Updating disulfide bridges.
INFO     PDB2PQR3.5.2:main.py:625 Debumping biomolecule.
INFO     PDB2PQR3.5.2:main.py:642 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.5.2:main.py:645 Debumping biomolecule (again).
INFO     PDB2PQR3.5.2:main.py:647 Optimizing hydrogen bonds
INFO     PDB2PQR3.5.2:main.py:659 Applying force field to biomolecule states.
INFO     PDB2PQR3.5.2:main.py:706 Regenerating headers.
INFO     PDB2PQR3.5.2:main.py:731 Regenerating PDB lines.
WARNING  PDB2PQR3.5.2:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.5.2:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:179 6 atoms have position differences > 0
INFO     common:common.py:191 0 atoms have position differences > 0.01
INFO     common:common.py:191 0 atoms have charge differences > 0
INFO     common:common.py:191 0 atoms have charge differences > 0.01
INFO     common:common.py:191 0 atoms have radius differences > 0
INFO     common:common.py:191 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-pbuilder1/pytest-0/test_other_options_1AFS_neutra0/output.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.5.2:main.py:763 Setting up molecule.
INFO     PDB2PQR3.5.2:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.5.2:main.py:767 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.5.2:main.py:603 Loading forcefield.
INFO     PDB2PQR3.5.2:main.py:607 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     PDB2PQR3.5.2:main.py:617 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:1051 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1051 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.5.2:main.py:622 Updating disulfide bridges.
INFO     PDB2PQR3.5.2:main.py:625 Debumping biomolecule.
INFO     PDB2PQR3.5.2:main.py:642 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.5.2:main.py:645 Debumping biomolecule (again).
INFO     PDB2PQR3.5.2:main.py:647 Optimizing hydrogen bonds
INFO     PDB2PQR3.5.2:main.py:659 Applying force field to biomolecule states.
INFO     PDB2PQR3.5.2:main.py:706 Regenerating headers.
INFO     PDB2PQR3.5.2:main.py:731 Regenerating PDB lines.
WARNING  PDB2PQR3.5.2:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.5.2:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:179 6 atoms have position differences > 0
INFO     common:common.py:191 0 atoms have position differences > 0.01
INFO     common:common.py:191 0 atoms have charge differences > 0
INFO     common:common.py:191 0 atoms have charge differences > 0.01
INFO     common:common.py:191 0 atoms have radius differences > 0
INFO     common:common.py:191 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-pbuilder1/pytest-0/test_other_options_1AFS_drop_w0/output.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.5.2:main.py:761 Dropping water from structure.
INFO     PDB2PQR3.5.2:main.py:763 Setting up molecule.
INFO     PDB2PQR3.5.2:main.py:408 Created biomolecule object with 642 residues and 5300 atoms.
INFO     PDB2PQR3.5.2:main.py:767 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.5.2:main.py:603 Loading forcefield.
INFO     PDB2PQR3.5.2:main.py:607 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     PDB2PQR3.5.2:main.py:617 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:1051 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1051 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.5.2:main.py:622 Updating disulfide bridges.
INFO     PDB2PQR3.5.2:main.py:625 Debumping biomolecule.
INFO     PDB2PQR3.5.2:main.py:642 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.5.2:main.py:645 Debumping biomolecule (again).
INFO     PDB2PQR3.5.2:main.py:647 Optimizing hydrogen bonds
INFO     PDB2PQR3.5.2:main.py:659 Applying force field to biomolecule states.
INFO     PDB2PQR3.5.2:main.py:706 Regenerating headers.
INFO     PDB2PQR3.5.2:main.py:731 Regenerating PDB lines.
WARNING  PDB2PQR3.5.2:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.5.2:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:179 6 atoms have position differences > 0
INFO     common:common.py:191 0 atoms have position differences > 0.01
INFO     common:common.py:191 0 atoms have charge differences > 0
INFO     common:common.py:191 0 atoms have charge differences > 0.01
INFO     common:common.py:191 0 atoms have radius differences > 0
INFO     common:common.py:191 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-pbuilder1/pytest-0/test_other_options_1AFS_userff0/output.log
INFO     PDB2PQR3.5.2:main.py:240 PDB2PQR v3.5.2: biomolecular structure conversion software.
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.5.2:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.5.2:main.py:752 Checking and transforming input arguments.
INFO     PDB2PQR3.5.2:main.py:756 Loading topology files.
INFO     PDB2PQR3.5.2:main.py:758 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.5.2:main.py:763 Setting up molecule.
INFO     PDB2PQR3.5.2:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.5.2:main.py:767 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.5.2:main.py:603 Loading forcefield.
INFO     PDB2PQR3.5.2:main.py:607 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     PDB2PQR3.5.2:main.py:617 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:1051 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1051 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.5.2:main.py:622 Updating disulfide bridges.
INFO     PDB2PQR3.5.2:main.py:625 Debumping biomolecule.
INFO     PDB2PQR3.5.2:main.py:642 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.5.2:main.py:645 Debumping biomolecule (again).
INFO     PDB2PQR3.5.2:main.py:647 Optimizing hydrogen bonds
INFO     PDB2PQR3.5.2:main.py:659 Applying force field to biomolecule states.
INFO     PDB2PQR3.5.2:main.py:706 Regenerating headers.
INFO     PDB2PQR3.5.2:main.py:731 Regenerating PDB lines.
WARNING  PDB2PQR3.5.2:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.5.2:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:179 6 atoms have position differences > 0
INFO     common:common.py:191 0 atoms have position differences > 0.01
INFO     common:common.py:191 0 atoms have charge differences > 0
INFO     common:common.py:191 0 atoms have charge differences > 0.01
INFO     common:common.py:191 0 atoms have radius differences > 0
INFO     common:common.py:191 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%]

============ 88 passed, 215 skipped, 4 xfailed in 68.37s (0:01:08) =============
   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:240: /usr/bin/python3 setup.py install --root /build/pdb2pqr-3.5.2+dfsg/debian/tmp 
running install
/usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
running build
running build_py
running install_lib
creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr
creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib
creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11
creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages
creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/run.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/inputgen.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/aa.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/debump.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/definitions.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/main.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/topology.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/psize.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/topology.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/peoe.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand
creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/__init__.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/peoe.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/mol2.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/mol2.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/cif.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/cif.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/__init__.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/debump.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/io.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/main.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/cells.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/pdb.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/structures.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/definitions.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/forcefield.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/aa.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/biomolecule.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/inputgen.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/config.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/residue.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/_version.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/psize.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/utilities.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/na.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/quatfit.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/_version.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/forcefield.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/na.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__main__.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/structures.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/cells.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/residue.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/config.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/biomolecule.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/utilities.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/pdb.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/io.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AMBER.names -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/CHARMM.names -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/SWANSON.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TOPOLOGY.xml -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AA.xml -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TYL06.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/NA.xml -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/SWANSON.names -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PATCHES.xml -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/HYDROGENS.xml -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PARSE.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PEOEPB.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TYL06.names -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PEOEPB.names -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PARSE.names -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AMBER.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/CHARMM.DAT -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/quatfit.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr
creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens
creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/__init__.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/structures.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/optimize.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/structures.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/optimize.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens
copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/run.py to run.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/inputgen.py to inputgen.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/aa.py to aa.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/debump.py to debump.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/definitions.py to definitions.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/main.py to main.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/topology.py to topology.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/psize.py to psize.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/topology.py to topology.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/peoe.py to peoe.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/mol2.py to mol2.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/cif.py to cif.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/_version.py to _version.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/forcefield.py to forcefield.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/na.py to na.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__main__.py to __main__.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/structures.py to structures.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/cells.py to cells.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/residue.py to residue.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/config.py to config.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/biomolecule.py to biomolecule.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/utilities.py to utilities.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/pdb.py to pdb.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/io.py to io.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/quatfit.py to quatfit.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/structures.py to structures.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/optimize.py to optimize.cpython-311.pyc
byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__init__.py to __init__.cpython-311.pyc
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 /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr-3.5.2.egg-info
Skipping SOURCES.txt
running install_scripts
Installing dx2cube script to /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/bin
Installing inputgen script to /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/bin
Installing pdb2pqr30 script to /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/bin
   dh_install -O--buildsystem=pybuild
   debian/rules override_dh_installdocs
make[1]: Entering directory '/build/pdb2pqr-3.5.2+dfsg'
dh_installdocs
dh_installdocs -p pdb2pqr-doc --doc-main-package pdb2pqr build/html
make[1]: Leaving directory '/build/pdb2pqr-3.5.2+dfsg'
   dh_sphinxdoc -O--buildsystem=pybuild
   dh_installchangelogs -O--buildsystem=pybuild
   dh_installexamples -O--buildsystem=pybuild
   debian/rules override_dh_installman
make[1]: Entering directory '/build/pdb2pqr-3.5.2+dfsg'
PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/dx2cube --no-info --version-string 3.5.2+dfsg > dx2cube.1
PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/inputgen --no-info --version-string 3.5.2+dfsg > inputgen.1
PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/pdb2pqr30 --no-info --version-string 3.5.2+dfsg > pdb2pqr30.1
dh_installman
make[1]: Leaving directory '/build/pdb2pqr-3.5.2+dfsg'
   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
dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_3.5.2+dfsg-3_all.deb'.
dpkg-deb: building package 'pdb2pqr-doc' in '../pdb2pqr-doc_3.5.2+dfsg-3_all.deb'.
dpkg-deb: building package 'python3-pdb2pqr' in '../python3-pdb2pqr_3.5.2+dfsg-3_all.deb'.
 dpkg-genbuildinfo --build=binary -O../pdb2pqr_3.5.2+dfsg-3_i386.buildinfo
 dpkg-genchanges --build=binary -O../pdb2pqr_3.5.2+dfsg-3_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/49292 and its subdirectories
I: Current time: Mon Jul  8 06:55:54 -12 2024
I: pbuilder-time-stamp: 1720464954