I: pbuilder: network access will be disabled during build I: Current time: Wed Apr 19 20:51:22 -12 2023 I: pbuilder-time-stamp: 1681980682 I: 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: 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/245127/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='8298141274324a2f8efab6c28b531a79' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='245127' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ByWQaoqZ/pbuilderrc_y6In --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ByWQaoqZ/b1 --logfile b1/build.log pdb2pqr_3.5.2+dfsg-3.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 12 08:05 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Feb 12 08:05 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/245127/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team 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 ... 19596 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-numba 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 65.3 MB of archives. After unpacking 287 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 fonts-lato all 2.0-2.1 [2696 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 13 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-2 [131 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 docutils-common all 0.19+dfsg-6 [127 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 help2man amd64 1.49.3 [198 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get: 66 http://deb.debian.org/debian bookworm/main amd64 python-babel-localedata all 2.10.3-1 [5615 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-3 [30.1 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 python3-babel all 2.10.3-1 [103 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 python3-roman all 3.3-3 [9880 B] Get: 80 http://deb.debian.org/debian bookworm/main amd64 python3-docutils all 0.19+dfsg-6 [382 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 python3-idna all 3.3-1 [39.4 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 83 http://deb.debian.org/debian bookworm/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 84 http://deb.debian.org/debian bookworm/main amd64 python3-markupsafe amd64 2.1.2-1+b1 [13.2 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 python3-jinja2 all 3.1.2-1 [119 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 python3-pandas-lib amd64 1.5.3+dfsg-2 [3499 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 python3-pdbx all 2.0.1-2 [17.4 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 python3-propka all 3.5.0-1 [65.6 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 python3-py all 1.11.0-1 [89.2 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 python3-pytest all 7.2.1-2 [236 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 python3-urllib3 all 1.26.12-1 [117 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 sphinx-common all 5.3.0-4 [653 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx all 5.3.0-4 [549 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx-rtd-theme all 1.2.0+dfsg-1 [27.7 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 python3-testfixtures all 7.0.4-1 [79.8 kB] Fetched 65.3 MB in 1s (45.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.0-2.1_all.deb ... Unpacking fonts-lato (2.0-2.1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-5_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... 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Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20386 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../01-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../03-openssl_3.0.8-1_amd64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../04-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../06-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../07-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../08-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../09-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../10-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../11-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../12-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../13-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../14-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../15-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... 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Preparing to unpack .../22-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../23-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../24-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../25-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../26-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../27-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../28-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../29-libxml2_2.9.14+dfsg-1.1+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../30-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../31-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../32-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../33-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package python3-lib2to3. 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Preparing to unpack .../40-help2man_1.49.3_amd64.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../41-libblas3_3.11.0-2_amd64.deb ... Unpacking libblas3:amd64 (3.11.0-2) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../42-libexpat1-dev_2.5.0-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.5.0-1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../43-libgfortran5_12.2.0-14_amd64.deb ... Unpacking libgfortran5:amd64 (12.2.0-14) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../44-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../45-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../46-libjs-sphinxdoc_5.3.0-4_all.deb ... Unpacking libjs-sphinxdoc (5.3.0-4) ... Selecting previously unselected package libjson-perl. Preparing to unpack .../47-libjson-perl_4.10000-1_all.deb ... Unpacking libjson-perl (4.10000-1) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../48-liblapack3_3.11.0-2_amd64.deb ... Unpacking liblapack3:amd64 (3.11.0-2) ... Selecting previously unselected package libpython3.11:amd64. Preparing to unpack .../49-libpython3.11_3.11.2-6_amd64.deb ... Unpacking libpython3.11:amd64 (3.11.2-6) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../50-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libpython3.11-dev:amd64. Preparing to unpack .../51-libpython3.11-dev_3.11.2-6_amd64.deb ... Unpacking libpython3.11-dev:amd64 (3.11.2-6) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../52-libpython3-dev_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.11.2-1+b1) ... Selecting previously unselected package python-babel-localedata. Preparing to unpack .../53-python-babel-localedata_2.10.3-1_all.deb ... Unpacking python-babel-localedata (2.10.3-1) ... Selecting previously unselected package python3-alabaster. Preparing to unpack .../54-python3-alabaster_0.7.12-1_all.deb ... Unpacking python3-alabaster (0.7.12-1) ... Selecting previously unselected package python3-attr. Preparing to unpack .../55-python3-attr_22.2.0-1_all.deb ... Unpacking python3-attr (22.2.0-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../56-python3-pkg-resources_66.1.1-1_all.deb ... Unpacking python3-pkg-resources (66.1.1-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../57-python3-tz_2022.7.1-3_all.deb ... Unpacking python3-tz (2022.7.1-3) ... Selecting previously unselected package python3-babel. Preparing to unpack .../58-python3-babel_2.10.3-1_all.deb ... Unpacking python3-babel (2.10.3-1) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../59-python3-certifi_2022.9.24-1_all.deb ... Unpacking python3-certifi (2022.9.24-1) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../60-python3-chardet_5.1.0+dfsg-2_all.deb ... Unpacking python3-chardet (5.1.0+dfsg-2) ... Selecting previously unselected package python3-charset-normalizer. Preparing to unpack .../61-python3-charset-normalizer_3.0.1-2_all.deb ... Unpacking python3-charset-normalizer (3.0.1-2) ... Selecting previously unselected package python3-six. Preparing to unpack .../62-python3-six_1.16.0-4_all.deb ... Unpacking python3-six (1.16.0-4) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../63-python3-dateutil_2.8.2-2_all.deb ... Unpacking python3-dateutil (2.8.2-2) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../64-python3.11-dev_3.11.2-6_amd64.deb ... Unpacking python3.11-dev (3.11.2-6) ... Selecting previously unselected package python3-dev. Preparing to unpack .../65-python3-dev_3.11.2-1+b1_amd64.deb ... Unpacking python3-dev (3.11.2-1+b1) ... Selecting previously unselected package python3-roman. Preparing to unpack .../66-python3-roman_3.3-3_all.deb ... Unpacking python3-roman (3.3-3) ... Selecting previously unselected package python3-docutils. Preparing to unpack .../67-python3-docutils_0.19+dfsg-6_all.deb ... Unpacking python3-docutils (0.19+dfsg-6) ... Selecting previously unselected package python3-idna. Preparing to unpack .../68-python3-idna_3.3-1_all.deb ... Unpacking python3-idna (3.3-1) ... Selecting previously unselected package python3-imagesize. Preparing to unpack .../69-python3-imagesize_1.4.1-1_all.deb ... Unpacking python3-imagesize (1.4.1-1) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../70-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-markupsafe. Preparing to unpack .../71-python3-markupsafe_2.1.2-1+b1_amd64.deb ... Unpacking python3-markupsafe (2.1.2-1+b1) ... Selecting previously unselected package python3-jinja2. Preparing to unpack .../72-python3-jinja2_3.1.2-1_all.deb ... Unpacking python3-jinja2 (3.1.2-1) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../73-python3-more-itertools_8.10.0-2_all.deb ... Unpacking python3-more-itertools (8.10.0-2) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../74-python3-numpy_1%3a1.24.2-1_amd64.deb ... Unpacking python3-numpy (1:1.24.2-1) ... 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Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (22.2.0-1) ... Setting up python3-propka (3.5.0-1) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up python3-babel (2.10.3-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3.11-dev (3.11.2-6) ... Setting up python3-charset-normalizer (3.0.1-2) ... Setting up python3-pytest (7.2.1-2) ... Setting up python3-alabaster (0.7.12-1) ... Setting up python3-pdbx (2.0.1-2) ... Setting up python3-testfixtures (7.0.4-1) ... Setting up python3-pygments (2.14.0+dfsg-1) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-pandas-lib:amd64 (1.5.3+dfsg-2) ... Setting up python3-pandas (1.5.3+dfsg-2) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.19+dfsg-6) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.19+dfsg-6) ... Setting up python3-sphinx (5.3.0-4) ... Setting up python3-sphinx-rtd-theme (1.2.0+dfsg-1) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> 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 dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem pybuild --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/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-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it rm -rf pdb2pqr.egg-info make[1]: Leaving directory '/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/utilities.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/structures.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/run.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/residue.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 copying pdb2pqr/psize.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/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/io.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/forcefield.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/debump.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/cif.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/biomolecule.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/_version.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/__init__.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/mol2.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand copying pdb2pqr/ligand/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand 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/PATCHES.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/HYDROGENS.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/TYL06.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/SWANSON.DAT -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/PEOEPB.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/CHARMM.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/TYL06.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/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 copying pdb2pqr/dat/CHARMM.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/AMBER.names -> /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat 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 : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))) [autosummary] generating autosummary for: api/aa.rst, api/biomolecule.rst, api/cells.rst, api/cif.rst, api/config.rst, api/debump.rst, api/definitions.rst, api/forcefield.rst, api/hydrogens.rst, api/index.rst, ..., formats/xml-names.rst, getting.rst, help.rst, index.rst, releases.rst, supporting.rst, using/algorithms.rst, using/examples.rst, using/index.rst, using/other-software.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 39 source files that are out of date updating environment: [new config] 39 added, 0 changed, 0 removed reading sources... [ 2%] api/aa reading sources... [ 5%] api/biomolecule reading sources... [ 7%] api/cells reading sources... [ 10%] api/cif reading sources... [ 12%] api/config reading sources... [ 15%] api/debump reading sources... [ 17%] api/definitions reading sources... [ 20%] api/forcefield reading sources... [ 23%] api/hydrogens reading sources... [ 25%] api/index reading sources... [ 28%] api/inputgen reading sources... [ 30%] api/io reading sources... [ 33%] api/ligand reading sources... [ 35%] api/main reading sources... [ 38%] api/na reading sources... [ 41%] api/pdb reading sources... [ 43%] api/psize reading sources... [ 46%] api/quatfit reading sources... [ 48%] api/residue reading sources... [ 51%] api/run reading sources... [ 53%] api/structures reading sources... [ 56%] api/topology reading sources... [ 58%] api/utilities reading sources... [ 61%] extending reading sources... [ 64%] formats/dat reading sources... [ 66%] formats/index reading sources... [ 69%] formats/mol2 reading sources... [ 71%] formats/pdb reading sources... [ 74%] formats/pqr reading sources... [ 76%] formats/xml-names reading sources... [ 79%] getting reading sources... [ 82%] help reading sources... [ 84%] index reading sources... [ 87%] releases reading sources... [ 89%] supporting reading sources... [ 92%] using/algorithms reading sources... [ 94%] using/examples reading sources... [ 97%] using/index reading sources... [100%] using/other-software looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 2%] api/aa writing output... [ 5%] api/biomolecule writing output... [ 7%] api/cells writing output... [ 10%] api/cif writing output... [ 12%] api/config writing output... [ 15%] api/debump writing output... [ 17%] api/definitions writing output... [ 20%] api/forcefield writing output... [ 23%] api/hydrogens writing output... [ 25%] api/index writing output... [ 28%] api/inputgen writing output... [ 30%] api/io writing output... [ 33%] api/ligand writing output... [ 35%] api/main writing output... [ 38%] api/na writing output... [ 41%] api/pdb writing output... [ 43%] api/psize writing output... [ 46%] api/quatfit writing output... [ 48%] api/residue writing output... [ 51%] api/run writing output... [ 53%] api/structures writing output... [ 56%] api/topology writing output... [ 58%] api/utilities writing output... [ 61%] extending writing output... [ 64%] formats/dat writing output... [ 66%] formats/index writing output... [ 69%] formats/mol2 writing output... [ 71%] formats/pdb writing output... [ 74%] formats/pqr writing output... [ 76%] formats/xml-names writing output... [ 79%] getting writing output... [ 82%] help writing output... [ 84%] index writing output... [ 87%] releases writing output... [ 89%] supporting writing output... [ 92%] using/algorithms writing output... [ 94%] using/examples writing output... [ 97%] using/index writing output... [100%] using/other-software generating indices... genindex py-modindex done highlighting module code... [ 4%] pdb2pqr.aa highlighting module code... [ 8%] pdb2pqr.biomolecule highlighting module code... [ 12%] pdb2pqr.cells highlighting module code... [ 16%] pdb2pqr.cif highlighting module code... [ 20%] pdb2pqr.debump highlighting module code... [ 24%] pdb2pqr.definitions highlighting module code... [ 28%] pdb2pqr.forcefield highlighting module code... [ 32%] pdb2pqr.hydrogens highlighting module code... [ 36%] pdb2pqr.hydrogens.optimize highlighting module code... [ 40%] pdb2pqr.hydrogens.structures highlighting module code... [ 44%] pdb2pqr.inputgen highlighting module code... [ 48%] pdb2pqr.io highlighting module code... [ 52%] pdb2pqr.ligand.mol2 highlighting module code... [ 56%] pdb2pqr.ligand.peoe highlighting module code... [ 60%] pdb2pqr.ligand.topology highlighting module code... [ 64%] pdb2pqr.main highlighting module code... [ 68%] pdb2pqr.na highlighting module code... [ 72%] pdb2pqr.pdb highlighting module code... [ 76%] pdb2pqr.psize highlighting module code... [ 80%] pdb2pqr.quatfit highlighting module code... [ 84%] pdb2pqr.residue highlighting module code... [ 88%] pdb2pqr.run highlighting module code... [ 92%] pdb2pqr.structures highlighting module code... [ 96%] pdb2pqr.topology highlighting module code... [100%] pdb2pqr.utilities writing additional pages... search done copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 2 warnings. The HTML pages are in build/html. make[1]: Leaving directory '/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 collected 307 items tests/core_test.py::test_short_pdb[1FAS] SKIPPED (not running tests ...) [ 0%] tests/core_test.py::test_short_pdb[1AQO] SKIPPED (not running tests ...) [ 0%] tests/core_test.py::test_short_pdb[4UN3] SKIPPED (not running tests ...) [ 0%] tests/core_test.py::test_short_pdb[1NAJ] SKIPPED (not running tests ...) [ 1%] tests/core_test.py::test_short_pdb[4E8M] SKIPPED (not running tests ...) [ 1%] tests/core_test.py::test_short_pdb[5D8V] SKIPPED (not running tests ...) [ 1%] tests/core_test.py::test_short_pdb[7BNA] SKIPPED (not running tests ...) [ 2%] tests/core_test.py::test_short_pdb[1K1I] SKIPPED (not running tests ...) [ 2%] tests/core_test.py::test_basic_cif[1FAS] SKIPPED (not running tests ...) 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[ 65%] tests/core_test.py::test_long_pdb[3LAA] SKIPPED (not running tests r...) [ 65%] tests/core_test.py::test_long_pdb[3ISU] SKIPPED (not running tests r...) [ 66%] tests/core_test.py::test_long_pdb[2J70] SKIPPED (not running tests r...) [ 66%] tests/core_test.py::test_long_pdb[3T1S] SKIPPED (not running tests r...) [ 66%] tests/core_test.py::test_long_pdb[4POY] SKIPPED (not running tests r...) [ 67%] tests/core_test.py::test_long_pdb[2HC8] SKIPPED (not running tests r...) [ 67%] tests/core_test.py::test_long_pdb[1PGX] SKIPPED (not running tests r...) [ 67%] tests/core_test.py::test_long_pdb[2GZV] SKIPPED (not running tests r...) [ 68%] tests/core_test.py::test_broken_backbone[4MGP] -------------------------------- 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[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 [ 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 [ 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/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 69%] tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 70%] 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_clean_whitespace.pqr] PASSED [ 70%] tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 71%] tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 71%] tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 71%] tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 71%] tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 72%] tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 72%] tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 72%] tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 73%] tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 73%] tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 73%] tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 74%] tests/io_test.py::test_read_pqr[tests/data/1HPX_with-ph=7.00_titration_state_method=propka_ligand=LIG_1HPX_ff=AMBER.pqr] PASSED [ 74%] tests/io_test.py::test_read_pqr[tests/data/dx2cube.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 214.84s (0:03:34) ============ 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 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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/quatfit.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/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__/_version.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/config.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/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__/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__/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__/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__/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__/__init__.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ 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/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/PEOEPB.names -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/SWANSON.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/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/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/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/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/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/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/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/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/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/TOPOLOGY.xml -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/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__/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/__pycache__/structures.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/__init__.cpython-311.pyc -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__init__.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/structures.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens creating /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/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__/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/__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/__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/ligand/peoe.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/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/__init__.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__main__.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/_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/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/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/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/cif.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/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/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/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/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/io.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/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/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/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/psize.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/quatfit.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/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/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/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/utilities.py -> /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__init__.py to __init__.cpython-311.pyc byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/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/structures.py to structures.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/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/topology.py to topology.cpython-311.pyc byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__init__.py to __init__.cpython-311.pyc byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__main__.py to __main__.cpython-311.pyc byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/_version.py to _version.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/biomolecule.py to biomolecule.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/cif.py to cif.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/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/forcefield.py to forcefield.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/io.py to io.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/na.py to na.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/psize.py to psize.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/residue.py to residue.cpython-311.pyc byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/run.py to run.cpython-311.pyc byte-compiling /build/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/structures.py to structures.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/utilities.py to utilities.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-doc' in '../pdb2pqr-doc_3.5.2+dfsg-3_all.deb'. dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_3.5.2+dfsg-3_all.deb'. dpkg-deb: building package 'python3-pdb2pqr' in '../python3-pdb2pqr_3.5.2+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../pdb2pqr_3.5.2+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../pdb2pqr_3.5.2+dfsg-3_amd64.changes 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/245127 and its subdirectories I: Current time: Wed Apr 19 20:56:53 -12 2023 I: pbuilder-time-stamp: 1681981013