I: pbuilder: network access will be disabled during build I: Current time: Tue May 20 20:12:19 +14 2025 I: pbuilder-time-stamp: 1747721539 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [pdb2pqr_3.6.1+dfsg-1.dsc] I: copying [./pdb2pqr_3.6.1+dfsg.orig.tar.xz] I: copying [./pdb2pqr_3.6.1+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Jun 12 17:36:50 2023 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting pdb2pqr in pdb2pqr-3.6.1+dfsg dpkg-source: info: unpacking pdb2pqr_3.6.1+dfsg.orig.tar.xz dpkg-source: info: unpacking pdb2pqr_3.6.1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip-network-tests.patch dpkg-source: info: applying unversioned_docutils.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/38577/tmp/hooks/D01_modify_environment starting debug: Running on ionos6-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 20 06:12 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/38577/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/38577/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=7a59f77cf70b424cba3855d62c48cde9 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=38577 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.lyiXSlBS/pbuilderrc_IsRX --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lyiXSlBS/b2 --logfile b2/build.log pdb2pqr_3.6.1+dfsg-1.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 17 17:48 /bin -> usr/bin I: user script /srv/workspace/pbuilder/38577/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team 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 ... 19874 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} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} python-babel-localedata{a} python3{a} python3-alabaster{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-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-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-sphinxcontrib.jquery{a} python3-testfixtures{a} python3-tz{a} python3-urllib3{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common libarchive-cpio-perl libjson-xs-perl libltdl-dev libmail-sendmail-perl libpaper-utils lynx python3-bottleneck python3-bs4 python3-html5lib python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pil python3-scipy python3-tables wget 0 packages upgraded, 109 newly installed, 0 to remove and 0 not upgraded. Need to get 75.1 MB of archives. After unpacking 335 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 liblocale-gettext-perl i386 1.07-6+b1 [15.3 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libpython3.11-minimal i386 3.11.8-1 [817 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.5.0-2+b2 [104 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 python3.11-minimal i386 3.11.8-1 [2087 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.11.6-1 [26.2 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 tzdata all 2024a-1 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-3 [69.1 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libreadline8 i386 8.2-3+b1 [171 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 libpython3.11-stdlib i386 3.11.8-1 [1821 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 python3.11 i386 3.11.8-1 [597 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.11.6-1 [9224 B] Get: 15 http://deb.debian.org/debian trixie/main i386 python3 i386 3.11.6-1 [26.2 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.2-1 [807 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.2-1 [2244 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 sgml-base all 1.31 [15.4 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 openssl i386 3.1.5-1 [1246 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20240203 [158 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3 [1195 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian trixie/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1 [118 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 python3-lib2to3 all 3.11.5-1 [77.5 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 python3-distutils all 3.11.5-1 [131 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 68.1.2-2 [468 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20240401 [107 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 xml-core all 0.19 [20.1 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 docutils-common all 0.20.1+dfsg-3 [128 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libexpat1-dev i386 2.5.0-2+b2 [159 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14-20240201-3 [733 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 libpython3.11 i386 3.11.8-1 [2009 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg-3+b1 [915 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 libpython3.11-dev i386 3.11.8-1 [4726 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 libpython3-dev i386 3.11.6-1 [9496 B] Get: 72 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.2-1 [1927 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 python-babel-localedata all 2.10.3-3 [5611 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 python3-tz all 2024.1-2 [30.9 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 python3-babel all 2.10.3-3 [100.0 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 python3-certifi all 2023.11.17-1 [155 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 python3-six all 1.16.0-6 [16.3 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 python3.11-dev i386 3.11.8-1 [509 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 python3-dev i386 3.11.6-1 [26.1 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 python3-roman all 3.3-3 [9880 B] Get: 85 http://deb.debian.org/debian trixie/main i386 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 python3-idna all 3.6-2 [37.0 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 python3-imagesize all 1.4.1-1 [6688 B] Get: 88 http://deb.debian.org/debian trixie/main i386 python3-iniconfig all 1.1.1-2 [6396 B] Get: 89 http://deb.debian.org/debian trixie/main i386 python3-markupsafe i386 2.1.5-1 [14.4 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 python3-jinja2 all 3.1.3-1 [119 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.2-1 [653 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 python3-numpy i386 1:1.24.2-2 [4879 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 python3-packaging all 24.0-1 [45.5 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 python3-pandas-lib i386 2.1.4+dfsg-5 [7492 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 python3-pandas all 2.1.4+dfsg-5 [3015 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 python3-pdbx all 2.0.1-2 [17.4 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 python3-pluggy all 1.4.0-1 [26.2 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 python3-propka all 3.5.1-1 [68.0 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 python3-pytest all 7.4.4-3 [239 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 python3-urllib3 all 1.26.18-2 [116 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 sphinx-common all 7.2.6-6 [702 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 python3-sphinx all 7.2.6-6 [552 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1021 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 108 http://deb.debian.org/debian trixie/main i386 python3-sphinx-rtd-theme all 2.0.0+dfsg-1 [28.3 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 python3-testfixtures all 8.1.0-1 [84.8 kB] Fetched 75.1 MB in 1s (58.4 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 ... 19874 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-6+b1_i386.deb ... Unpacking liblocale-gettext-perl (1.07-6+b1) ... Selecting previously unselected package libpython3.11-minimal:i386. 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Setting up libmagic1:i386 (1:5.45-2+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up python-babel-localedata (2.10.3-3) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue May 20 06:12:43 UTC 2025. Universal Time is now: Tue May 20 06:12:43 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libexpat1-dev:i386 (2.5.0-2+b2) ... Setting up autopoint (0.21-14) ... Setting up libgfortran5:i386 (14-20240201-3) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg-3+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:i386 (0.0.8-1+b1) ... 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Setting up liblapack3:i386 (3.12.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libreadline8:i386 (8.2-3+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up xml-core (0.19) ... Setting up libpython3.12-stdlib:i386 (3.12.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.8-1) ... Setting up python3.12 (3.12.2-1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up sphinx-common (7.2.6-6) ... Setting up libpython3-stdlib:i386 (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up libpython3.11:i386 (3.11.8-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.6-1) ... Setting up python3-markupsafe (2.1.5-1) ... Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.0-1) ... Setting up python3-certifi (2023.11.17-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libpython3.11-dev:i386 (3.11.8-1) ... Setting up python3-idna (3.6-2) ... Setting up python3-urllib3 (1.26.18-2) ... Setting up python3-pluggy (1.4.0-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-propka (3.5.1-1) ... Setting up libpython3-dev:i386 (3.11.6-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-babel (2.10.3-3) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3.11-dev (3.11.8-1) ... Setting up python3-charset-normalizer (3.3.2-1) ... Setting up python3-pytest (7.4.4-3) ... Setting up python3-alabaster (0.7.12-1) ... Setting up python3-pdbx (2.0.1-2) ... Setting up python3-testfixtures (8.1.0-1) ... Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-dev (3.11.6-1) ... Setting up python3-requests (2.31.0+dfsg-1) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up dh-python (6.20240401) ... Setting up python3-pandas-lib:i386 (2.1.4+dfsg-5) ... Setting up python3-pandas (2.1.4+dfsg-5) ... Processing triggers for libc-bin (2.37-15) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-sphinx (7.2.6-6) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-rtd-theme (2.0.0+dfsg-1) ... Processing triggers for ca-certificates (20240203) ... 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: user script /srv/workspace/pbuilder/38577/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/38577/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/pdb2pqr-3.6.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../pdb2pqr_3.6.1+dfsg-1_source.changes dpkg-buildpackage: info: source package pdb2pqr dpkg-buildpackage: info: source version 3.6.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --buildsystem pybuild --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/pdb2pqr-3.6.1+dfsg' dh_auto_clean I: pybuild base:311: python3.11 setup.py clean running clean removing '/build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-i686' 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/reproducible-path/pdb2pqr-3.6.1+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:311: python3.11 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/pdb2pqr-3.6.1+dfsg' dh_auto_build I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/run.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/inputgen.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/aa.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/debump.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/definitions.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/main.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/psize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/cif.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/_version.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/forcefield.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/na.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/__main__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/cells.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/residue.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/config.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/biomolecule.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/utilities.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/pdb.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/io.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr copying pdb2pqr/quatfit.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand copying pdb2pqr/ligand/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand copying pdb2pqr/ligand/peoe.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand copying pdb2pqr/ligand/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand copying pdb2pqr/ligand/mol2.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens copying pdb2pqr/hydrogens/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens copying pdb2pqr/hydrogens/optimize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens copying pdb2pqr/hydrogens/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/TOPOLOGY.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/AA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/NA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/PATCHES.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/HYDROGENS.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/SWANSON.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/TYL06.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/PARSE.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/PEOEPB.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/AMBER.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/CHARMM.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/AMBER.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/CHARMM.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/SWANSON.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/TYL06.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/PEOEPB.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat copying pdb2pqr/dat/PARSE.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat PYTHONPATH=. python3 -m sphinx -N -bhtml docs/source build/html Running Sphinx v7.2.6 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 writing output... building [html]: targets for 39 source files that are out of date updating environment: [new config] 39 added, 0 changed, 0 removed reading sources... [ 3%] api/aa reading sources... [ 5%] api/biomolecule reading sources... [ 8%] api/cells reading sources... [ 10%] api/cif reading sources... [ 13%] api/config reading sources... [ 15%] api/debump reading sources... [ 18%] api/definitions reading sources... [ 21%] api/forcefield reading sources... [ 23%] api/hydrogens reading sources... [ 26%] api/index reading sources... [ 28%] api/inputgen reading sources... [ 31%] api/io reading sources... [ 33%] api/ligand reading sources... [ 36%] api/main reading sources... [ 38%] api/na reading sources... [ 41%] api/pdb reading sources... [ 44%] api/psize reading sources... [ 46%] api/quatfit reading sources... [ 49%] api/residue reading sources... [ 51%] api/run reading sources... [ 54%] api/structures reading sources... [ 56%] api/topology reading sources... [ 59%] api/utilities reading sources... [ 62%] extending reading sources... [ 64%] formats/dat reading sources... [ 67%] formats/index reading sources... [ 69%] formats/mol2 reading sources... [ 72%] formats/pdb reading sources... [ 74%] formats/pqr reading sources... [ 77%] formats/xml-names reading sources... [ 79%] getting reading sources... [ 82%] help reading sources... [ 85%] index reading sources... [ 87%] releases reading sources... [ 90%] supporting reading sources... [ 92%] using/algorithms reading sources... [ 95%] 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 copying assets... copying static files... done copying extra files... done done writing output... [ 3%] api/aa writing output... [ 5%] api/biomolecule writing output... [ 8%] api/cells writing output... [ 10%] api/cif writing output... [ 13%] api/config writing output... [ 15%] api/debump writing output... [ 18%] api/definitions writing output... [ 21%] api/forcefield writing output... [ 23%] api/hydrogens writing output... [ 26%] api/index writing output... [ 28%] api/inputgen writing output... [ 31%] api/io writing output... [ 33%] api/ligand writing output... [ 36%] api/main writing output... [ 38%] api/na writing output... [ 41%] api/pdb writing output... [ 44%] api/psize writing output... [ 46%] api/quatfit writing output... [ 49%] api/residue writing output... [ 51%] api/run writing output... [ 54%] api/structures writing output... [ 56%] api/topology writing output... [ 59%] api/utilities writing output... [ 62%] extending writing output... [ 64%] formats/dat writing output... [ 67%] formats/index writing output... [ 69%] formats/mol2 writing output... [ 72%] formats/pdb writing output... [ 74%] formats/pqr writing output... [ 77%] formats/xml-names writing output... [ 79%] getting writing output... [ 82%] help writing output... [ 85%] index writing output... [ 87%] releases writing output... [ 90%] supporting writing output... [ 92%] using/algorithms writing output... [ 95%] 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 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/reproducible-path/pdb2pqr-3.6.1+dfsg' dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build; python3.11 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.11.8, pytest-7.4.4, pluggy-1.4.0 rootdir: /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build configfile: pytest.ini ----------------------------- live log collection ------------------------------ WARNING py.warnings:warnings.py:110 /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/tests/core_test.py:81: PytestUnknownMarkWarning: Unknown pytest.mark.long_test - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html @pytest.mark.long_test ERROR regression_test:regression_test.py:173 Need to reinstate the --apbs-input test with a temporary directory as path collected 316 items tests/core_test.py::test_short_pdb[1K1I] SKIPPED (not running tests ...) [ 0%] tests/core_test.py::test_short_pdb[1FAS] SKIPPED (not running tests ...) [ 0%] tests/core_test.py::test_short_pdb[4E8M] SKIPPED (not running tests ...) [ 0%] tests/core_test.py::test_short_pdb[7BNA] SKIPPED (not running tests ...) [ 1%] tests/core_test.py::test_short_pdb[1NAJ] SKIPPED (not running tests ...) [ 1%] tests/core_test.py::test_short_pdb[4UN3] SKIPPED (not running tests ...) [ 1%] tests/core_test.py::test_short_pdb[1AQO] SKIPPED (not running tests ...) [ 2%] tests/core_test.py::test_short_pdb[5D8V] SKIPPED (not running tests ...) [ 2%] tests/core_test.py::test_basic_cif[1K1I] SKIPPED (not running tests ...) 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INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 XFAIL [ 66%] tests/core_test.py::test_broken_backbone[4MGP] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_broken_backbone_4MGP_0/4MGP.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP XFAIL [ 66%] tests/core_test.py::test_broken_backbone[1EJG] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_broken_backbone_1EJG_0/1EJG.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG XFAIL [ 67%] tests/core_test.py::test_broken_backbone[3U7T] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_broken_backbone_3U7T_0/3U7T.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T XFAIL [ 67%] tests/core_test.py::test_protonated_terminals[C-terminal HID] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. INFO common:common.py:198 0 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 67%] tests/core_test.py::test_cyclic_peptide[Cyclic peptide] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. INFO common:common.py:198 0 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 68%] tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 68%] tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 68%] tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 68%] tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 69%] tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 69%] 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 [ 69%] tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 70%] tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 70%] tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 70%] tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 71%] tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 71%] tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 71%] tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 72%] tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 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_drop-water_ff=AMBER.pqr] PASSED [ 73%] tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 73%] tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 73%] tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 74%] tests/io_test.py::test_read_qcd PASSED [ 74%] tests/io_test.py::test_dx2cube -------------------------------- live log call --------------------------------- INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-pbuilder2/pytest-0/test_dx2cube0/test.cube... INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-pbuilder2/pytest-0/test_dx2cube0/test.cube... INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... INFO io_test:io_test.py:68 No differences found in output PASSED [ 74%] tests/ligand_test.py::test_peoe_charges -------------------------------- live log call --------------------------------- WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. PASSED [ 75%] tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] -------------------------------- live log call --------------------------------- WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 PASSED [ 75%] tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] -------------------------------- live log call --------------------------------- WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 PASSED [ 75%] tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] -------------------------------- live log call --------------------------------- WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 PASSED [ 75%] tests/ligand_test.py::test_assign_parameters[acetate.mol2] -------------------------------- live log call --------------------------------- INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 PASSED [ 76%] tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] -------------------------------- live log call --------------------------------- INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 PASSED [ 76%] tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] -------------------------------- live log call --------------------------------- WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 PASSED [ 76%] tests/ligand_test.py::test_assign_parameters[adp.mol2] -------------------------------- live log call --------------------------------- WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 PASSED [ 77%] tests/ligand_test.py::test_assign_parameters[anthracene.mol2] -------------------------------- live log call --------------------------------- INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 PASSED [ 77%] tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] -------------------------------- live log call --------------------------------- INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 PASSED [ 77%] tests/ligand_test.py::test_assign_parameters[ethanol.mol2] -------------------------------- live log call --------------------------------- INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 PASSED [ 78%] tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] -------------------------------- live log call --------------------------------- INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 PASSED [ 78%] tests/ligand_test.py::test_assign_parameters[glycerol.mol2] -------------------------------- live log call --------------------------------- INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 PASSED [ 78%] tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] -------------------------------- live log call --------------------------------- INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 PASSED [ 79%] tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] -------------------------------- live log call --------------------------------- INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 PASSED [ 79%] tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] -------------------------------- live log call --------------------------------- WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 PASSED [ 79%] tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] -------------------------------- live log call --------------------------------- WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. PASSED [ 80%] tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] -------------------------------- live log call --------------------------------- WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. PASSED [ 80%] tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] -------------------------------- live log call --------------------------------- WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. PASSED [ 80%] tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] -------------------------------- live log call --------------------------------- WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. PASSED [ 81%] tests/ligand_test.py::test_formal_charge[adp.mol2] -------------------------------- live log call --------------------------------- WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. PASSED [ 81%] tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] -------------------------------- live log call --------------------------------- WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. PASSED [ 84%] tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] tests/regression_test.py::test_basic[1AFS basic local] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_basic_1AFS_basic_local_0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. WARNING common:common.py:186 6 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 95%] tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_forcefields_1AFS_whitespa0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. WARNING common:common.py:186 6 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 95%] tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_forcefields_1AFS_whitespa1/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. WARNING common:common.py:186 5 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 95%] tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_forcefields_1AFS_whitespa2/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. WARNING common:common.py:186 6 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 96%] tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_forcefields_1AFS_whitespa3/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. WARNING common:common.py:186 6 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 96%] tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_forcefields_1AFS_whitespa4/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. WARNING common:common.py:186 6 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 96%] tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_forcefields_1AFS_whitespa5/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. WARNING common:common.py:186 6 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 97%] tests/regression_test.py::test_other_options[1AFS whitespace clean] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_other_options_1AFS_whites0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps. INFO common:common.py:198 0 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 97%] tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_other_options_1A1P_assign0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. INFO common:common.py:198 0 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 97%] tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_other_options_1A1P_nodebu0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. INFO common:common.py:198 0 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 98%] tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_other_options_1AFS_chain_0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. WARNING common:common.py:186 6 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 98%] tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_other_options_1AFS_neutra0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. WARNING common:common.py:186 6 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 98%] tests/regression_test.py::test_other_options[1AFS drop-water AMBER] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_other_options_1AFS_drop_w0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. WARNING common:common.py:186 6 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 99%] tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_other_options_1AFS_userff0/output.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. WARNING common:common.py:186 6 atoms have position differences > 0 INFO common:common.py:198 0 atoms have position differences > 0.01 INFO common:common.py:198 0 atoms have charge differences > 0 INFO common:common.py:198 0 atoms have charge differences > 0.01 INFO common:common.py:198 0 atoms have radius differences > 0 INFO common:common.py:198 0 atoms have radius differences > 0.01 PASSED [ 99%] tests/test_version.py::test_version_exists PASSED [ 99%] tests/test_version.py::test_version PASSED [100%] ============ 92 passed, 220 skipped, 4 xfailed in 65.27s (0:01:05) ============= 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:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running install_lib creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11 creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/.pytest_cache/.gitignore -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/.pytest_cache/v/cache/stepwise -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/.pytest_cache/v/cache/nodeids -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/.pytest_cache/CACHEDIR.TAG -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/.pytest_cache/README.md -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/.pytest_cache creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/run.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/inputgen.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/aa.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/debump.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/definitions.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/main.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/psize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/peoe.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/peoe.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__pycache__/mol2.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/ligand/mol2.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/cif.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/cif.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/debump.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/io.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/main.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/cells.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/pdb.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/structures.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/definitions.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/forcefield.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/aa.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/biomolecule.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/inputgen.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/config.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/residue.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/_version.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/psize.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/utilities.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/na.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__pycache__/quatfit.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/_version.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/forcefield.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/na.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__main__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/cells.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/residue.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/config.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/biomolecule.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/utilities.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/pdb.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/io.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AMBER.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/CHARMM.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/SWANSON.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TOPOLOGY.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TYL06.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/NA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/SWANSON.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PATCHES.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/HYDROGENS.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PARSE.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PEOEPB.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/TYL06.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PEOEPB.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/PARSE.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/AMBER.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/dat/CHARMM.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/quatfit.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/structures.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__pycache__/optimize.cpython-311.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/optimize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.11/build/pdb2pqr/hydrogens/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/run.py to run.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/inputgen.py to inputgen.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/aa.py to aa.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/debump.py to debump.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/definitions.py to definitions.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/main.py to main.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/topology.py to topology.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/psize.py to psize.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/topology.py to topology.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/peoe.py to peoe.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/ligand/mol2.py to mol2.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/cif.py to cif.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/_version.py to _version.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/forcefield.py to forcefield.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/na.py to na.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__main__.py to __main__.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/structures.py to structures.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/cells.py to cells.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/residue.py to residue.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/config.py to config.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/biomolecule.py to biomolecule.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/utilities.py to utilities.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/pdb.py to pdb.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/io.py to io.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/quatfit.py to quatfit.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/structures.py to structures.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/optimize.py to optimize.cpython-311.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr/hydrogens/__init__.py to __init__.cpython-311.pyc running install_egg_info running egg_info creating pdb2pqr.egg-info writing pdb2pqr.egg-info/PKG-INFO writing dependency_links to pdb2pqr.egg-info/dependency_links.txt writing entry points to pdb2pqr.egg-info/entry_points.txt writing requirements to pdb2pqr.egg-info/requires.txt writing top-level names to pdb2pqr.egg-info/top_level.txt writing manifest file 'pdb2pqr.egg-info/SOURCES.txt' reading manifest file 'pdb2pqr.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'pdb2pka' adding license file 'LICENSE.md' adding license file 'COPYING' writing manifest file 'pdb2pqr.egg-info/SOURCES.txt' Copying pdb2pqr.egg-info to /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.11/dist-packages/pdb2pqr-3.6.1.egg-info Skipping SOURCES.txt running install_scripts Installing dx2cube script to /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/bin Installing inputgen script to /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/bin Installing pdb2pqr script to /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/bin Installing pdb2pqr30 script to /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/bin dh_install -O--buildsystem=pybuild debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/pdb2pqr-3.6.1+dfsg' dh_installdocs dh_installdocs -p pdb2pqr-doc --doc-main-package pdb2pqr build/html make[1]: Leaving directory '/build/reproducible-path/pdb2pqr-3.6.1+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/reproducible-path/pdb2pqr-3.6.1+dfsg' PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/dx2cube --no-info --version-string 3.6.1+dfsg > dx2cube.1 PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/inputgen --no-info --version-string 3.6.1+dfsg > inputgen.1 PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/pdb2pqr30 --no-info --version-string 3.6.1+dfsg > pdb2pqr30.1 dh_installman make[1]: Leaving directory '/build/reproducible-path/pdb2pqr-3.6.1+dfsg' dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package pdb2pqr-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_3.6.1+dfsg-1_all.deb'. dpkg-deb: building package 'pdb2pqr-doc' in '../pdb2pqr-doc_3.6.1+dfsg-1_all.deb'. dpkg-deb: building package 'python3-pdb2pqr' in '../python3-pdb2pqr_3.6.1+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../pdb2pqr_3.6.1+dfsg-1_i386.buildinfo dpkg-genchanges --build=binary -O../pdb2pqr_3.6.1+dfsg-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/38577/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/38577/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/38577 and its subdirectories I: Current time: Tue May 20 20:14:37 +14 2025 I: pbuilder-time-stamp: 1747721677