I: pbuilder: network access will be disabled during build I: Current time: Wed Nov 13 09:41:42 +14 2024 I: pbuilder-time-stamp: 1731440502 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [pdb2pqr_3.6.1+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/5800/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. 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 Nov 12 19:41 /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/5800/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/5800/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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=0e4d4fd08e6f4a8cbc4b046a2051c2f4 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=5800 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.rQzwZEyz/pbuilderrc_6CHT --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rQzwZEyz/b2 --logfile b2/build.log pdb2pqr_3.6.1+dfsg-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/5800/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: arm64 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 ... 20088 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} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libpipeline1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} libtirpc-common{a} libtirpc3t64{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-autocommand{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-dateutil{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pdbx{a} python3-pkg-resources{a} python3-pluggy{a} python3-propka{a} python3-pygments{a} python3-pytest{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-testfixtures{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-urllib3{a} python3-zipp{a} python3.12{a} python3.12-dev{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 krb5-locales 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, 120 newly installed, 0 to remove and 0 not upgraded. Need to get 64.9 MB of archives. After unpacking 296 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.7-3 [808 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.7-3 [1940 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.6-1 [26.7 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-3 [255 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 14 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.7-3 [1902 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.7-3 [671 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B] Get: 24 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.6-1 [27.8 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-10 [96.5 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2 [630 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.2.0-1 [731 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20241024 [109 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-3+b1 [98.9 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-3+b1 [1812 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libpython3.12t64 arm64 3.12.7-3 [1982 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libpython3.12-dev arm64 3.12.7-3 [4792 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.12.6-1 [9952 B] Get: 85 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.14.0-1 [111 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 90 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer arm64 3.4.0-1 [112 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 python3.12-dev arm64 3.12.7-3 [505 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.12.6-1 [26.1 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 python3-roman all 4.2-1 [10.4 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.8-2 [41.6 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 100 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 101 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1+b2 [13.8 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.1-1 [45.8 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [3746 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 python3-pdbx all 2.0.1-2 [17.4 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 python3-propka all 3.5.1-2 [68.2 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 7.4.7-4 [731 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 7.4.7-4 [588 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1022 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 119 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [29.5 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 python3-testfixtures all 8.3.0-2 [87.2 kB] Fetched 64.9 MB in 1s (126 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 ... 20088 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_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.12-minimal:arm64. 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Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. 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Selecting previously unselected package python3-packaging. Preparing to unpack .../80-python3-packaging_24.1-1_all.deb ... Unpacking python3-packaging (24.1-1) ... Selecting previously unselected package python3-pandas-lib:arm64. Preparing to unpack .../81-python3-pandas-lib_2.2.3+dfsg-5_arm64.deb ... Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../82-python3-pandas_2.2.3+dfsg-5_all.deb ... Unpacking python3-pandas (2.2.3+dfsg-5) ... Selecting previously unselected package python3-pdbx. Preparing to unpack .../83-python3-pdbx_2.0.1-2_all.deb ... Unpacking python3-pdbx (2.0.1-2) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../84-python3-pluggy_1.5.0-1_all.deb ... Unpacking python3-pluggy (1.5.0-1) ... Selecting previously unselected package python3-propka. Preparing to unpack .../85-python3-propka_3.5.1-2_all.deb ... Unpacking python3-propka (3.5.1-2) ... 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Unpacking sphinx-common (7.4.7-4) ... Selecting previously unselected package python3-sphinx. Preparing to unpack .../92-python3-sphinx_7.4.7-4_all.deb ... Unpacking python3-sphinx (7.4.7-4) ... Selecting previously unselected package sphinx-rtd-theme-common. Preparing to unpack .../93-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... Selecting previously unselected package python3-sphinxcontrib.jquery. Preparing to unpack .../94-python3-sphinxcontrib.jquery_4.1-5_all.deb ... Unpacking python3-sphinxcontrib.jquery (4.1-5) ... Selecting previously unselected package python3-sphinx-rtd-theme. Preparing to unpack .../95-python3-sphinx-rtd-theme_3.0.1+dfsg-1_all.deb ... Unpacking python3-sphinx-rtd-theme (3.0.1+dfsg-1) ... Selecting previously unselected package python3-testfixtures. Preparing to unpack .../96-python3-testfixtures_8.3.0-2_all.deb ... Unpacking python3-testfixtures (8.3.0-2) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up fonts-lato (2.015-1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-10) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:arm64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up python-babel-localedata (2.14.0-1) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Nov 12 19:42:33 UTC 2024. Universal Time is now: Tue Nov 12 19:42:33 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libexpat1-dev:arm64 (2.6.4-1) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libgfortran5:arm64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libjson-perl (4.10000-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.3.2-2) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up sphinx-common (7.4.7-4) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up libpython3.12-stdlib:arm64 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libpython3.12t64:arm64 (3.12.7-3) ... Setting up libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:arm64 (3.12.7-3) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b2) ... Setting up python3-tz (2024.1-2) ... Setting up python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.1-1) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-idna (3.8-2) ... Setting up python3.12-dev (3.12.7-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-propka (3.5.1-2) ... Setting up libpython3-dev:arm64 (3.12.6-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-charset-normalizer (3.4.0-1) ... Setting up python3-pytest (8.3.3-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-pdbx (2.0.1-2) ... Setting up python3-testfixtures (8.3.0-2) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up dh-python (6.20241024) ... Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (7.4.7-4) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-rtd-theme (3.0.1+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/5800/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/5800/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 arm64 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: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running clean removing '/build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' 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: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) 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 /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) running build running build_py creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/__main__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/_version.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/aa.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/biomolecule.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/cells.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/cif.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/config.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/debump.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/definitions.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/forcefield.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/inputgen.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/io.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/main.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/na.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/pdb.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/psize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/quatfit.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/residue.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/run.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr copying pdb2pqr/utilities.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/hydrogens copying pdb2pqr/hydrogens/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/hydrogens copying pdb2pqr/hydrogens/optimize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/hydrogens copying pdb2pqr/hydrogens/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/hydrogens creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/ligand copying pdb2pqr/ligand/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/ligand copying pdb2pqr/ligand/mol2.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/ligand copying pdb2pqr/ligand/peoe.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/ligand copying pdb2pqr/ligand/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/ligand creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/AA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/HYDROGENS.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/NA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/PATCHES.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/TOPOLOGY.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/AMBER.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/CHARMM.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/PARSE.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/PEOEPB.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/SWANSON.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/TYL06.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/AMBER.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/CHARMM.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/PARSE.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/PEOEPB.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/SWANSON.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat copying pdb2pqr/dat/TYL06.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat PYTHONPATH=. python3 -m sphinx -N -bhtml docs/source build/html Running Sphinx v7.4.7 loading translations [en]... done WARNING: html_static_path entry '_static' does not exist loading intersphinx inventory 'python' 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('Unable to 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... 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[ 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... 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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_3.12/build; python3.12 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 rootdir: /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build configfile: pytest.ini plugins: typeguard-4.4.1 ----------------------------- live log collection ------------------------------ WARNING py.warnings:warnings.py:112 /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/tests/core_test.py:81: PytestUnknownMarkWarning: Unknown pytest.mark.long_test - is this a typo? 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[ 44%] tests/core_test.py::test_long_pdb[1AFS] SKIPPED (not running tests r...) [ 44%] tests/core_test.py::test_long_pdb[2G7O] SKIPPED (not running tests r...) [ 45%] tests/core_test.py::test_long_pdb[2J9V] SKIPPED (not running tests r...) [ 45%] tests/core_test.py::test_long_pdb[1R7J] SKIPPED (not running tests r...) [ 45%] tests/core_test.py::test_long_pdb[2JCP] SKIPPED (not running tests r...) [ 46%] tests/core_test.py::test_long_pdb[3FH2] SKIPPED (not running tests r...) [ 46%] tests/core_test.py::test_long_pdb[3RJS] SKIPPED (not running tests r...) [ 46%] tests/core_test.py::test_long_pdb[2YXF] SKIPPED (not running tests r...) [ 47%] tests/core_test.py::test_long_pdb[3NX6] SKIPPED (not running tests r...) [ 47%] tests/core_test.py::test_long_pdb[4PGR] SKIPPED (not running tests r...) [ 47%] tests/core_test.py::test_long_pdb[2ERW] SKIPPED (not running tests r...) [ 48%] tests/core_test.py::test_long_pdb[2GZV] SKIPPED (not running tests r...) [ 48%] tests/core_test.py::test_long_pdb[1YIB] SKIPPED (not running tests r...) [ 48%] tests/core_test.py::test_long_pdb[2IWN] SKIPPED (not running tests r...) [ 49%] tests/core_test.py::test_long_pdb[2REY] SKIPPED (not running tests r...) [ 49%] tests/core_test.py::test_long_pdb[3CQT] SKIPPED (not running tests r...) [ 49%] tests/core_test.py::test_long_pdb[4TTW] SKIPPED (not running tests r...) [ 50%] tests/core_test.py::test_long_pdb[4EO0] SKIPPED (not running tests r...) [ 50%] tests/core_test.py::test_long_pdb[1B0X] SKIPPED (not running tests r...) [ 50%] tests/core_test.py::test_long_pdb[2CGQ] SKIPPED (not running tests r...) [ 50%] tests/core_test.py::test_long_pdb[1ZZK] SKIPPED (not running tests r...) [ 51%] tests/core_test.py::test_long_pdb[3JTE] SKIPPED (not running tests r...) [ 51%] tests/core_test.py::test_long_pdb[2OO2] SKIPPED (not running tests r...) [ 51%] tests/core_test.py::test_long_pdb[3SO2] SKIPPED (not running tests r...) [ 52%] tests/core_test.py::test_long_pdb[3T1S] SKIPPED (not running tests r...) [ 52%] tests/core_test.py::test_long_pdb[3HRO] SKIPPED (not running tests r...) [ 52%] tests/core_test.py::test_long_pdb[3S0A] SKIPPED (not running tests r...) [ 53%] tests/core_test.py::test_long_pdb[5V0O] SKIPPED (not running tests r...) [ 53%] tests/core_test.py::test_long_pdb[2EBB] SKIPPED (not running tests r...) [ 53%] tests/core_test.py::test_long_pdb[2FRG] SKIPPED (not running tests r...) [ 54%] tests/core_test.py::test_long_pdb[2ESK] SKIPPED (not running tests r...) [ 54%] tests/core_test.py::test_long_pdb[3KZD] SKIPPED (not running tests r...) [ 54%] tests/core_test.py::test_long_pdb[4CRH] SKIPPED (not running tests r...) [ 55%] tests/core_test.py::test_long_pdb[3KT2] SKIPPED (not running tests r...) [ 55%] tests/core_test.py::test_long_pdb[4O7Q] SKIPPED (not running tests r...) [ 55%] tests/core_test.py::test_long_pdb[1PGX] SKIPPED (not running tests r...) [ 56%] tests/core_test.py::test_long_pdb[5DV8] SKIPPED (not running tests r...) [ 56%] tests/core_test.py::test_long_pdb[1X91] SKIPPED (not running tests r...) [ 56%] tests/core_test.py::test_long_pdb[2FD4] SKIPPED (not running tests r...) [ 56%] tests/core_test.py::test_long_pdb[3V1A] SKIPPED (not running tests r...) [ 57%] tests/core_test.py::test_long_pdb[2HDZ] SKIPPED (not running tests r...) [ 57%] tests/core_test.py::test_long_pdb[2IBL] SKIPPED (not running tests r...) [ 57%] tests/core_test.py::test_long_pdb[1I2T] SKIPPED (not running tests r...) [ 58%] tests/core_test.py::test_long_pdb[1YZM] SKIPPED (not running tests r...) [ 58%] tests/core_test.py::test_long_pdb[1TIG] SKIPPED (not running tests r...) [ 58%] tests/core_test.py::test_long_pdb[3LAA] SKIPPED (not running tests r...) [ 59%] tests/core_test.py::test_long_pdb[1TG0] SKIPPED (not running tests r...) [ 59%] tests/core_test.py::test_long_pdb[3WFV] SKIPPED (not running tests r...) [ 59%] tests/core_test.py::test_long_pdb[3ZHI] SKIPPED (not running tests r...) [ 60%] tests/core_test.py::test_long_pdb[1SJV] SKIPPED (not running tests r...) [ 60%] tests/core_test.py::test_long_pdb[1TVQ] SKIPPED (not running tests r...) [ 60%] tests/core_test.py::test_long_pdb[1TEN] SKIPPED (not running tests r...) [ 61%] tests/core_test.py::test_long_pdb[1FAS] SKIPPED (not running tests r...) [ 61%] tests/core_test.py::test_long_pdb[5EE2] SKIPPED (not running tests r...) [ 61%] tests/core_test.py::test_long_pdb[2PII] SKIPPED (not running tests r...) [ 62%] tests/core_test.py::test_long_pdb[3H0X] SKIPPED (not running tests r...) [ 62%] tests/core_test.py::test_long_pdb[2CWR] SKIPPED (not running tests r...) [ 62%] tests/core_test.py::test_long_pdb[1X6J] SKIPPED (not running tests r...) [ 62%] tests/core_test.py::test_long_pdb[4LJ1] SKIPPED (not running tests r...) [ 63%] tests/core_test.py::test_long_pdb[1UG4] SKIPPED (not running tests r...) [ 63%] tests/core_test.py::test_long_pdb[2BYG] SKIPPED (not running tests r...) [ 63%] tests/core_test.py::test_long_pdb[3DVI] SKIPPED (not running tests r...) [ 64%] tests/core_test.py::test_long_pdb[1ZLM] SKIPPED (not running tests r...) [ 64%] tests/core_test.py::test_long_pdb[4ZQA] SKIPPED (not running tests r...) [ 64%] tests/core_test.py::test_long_pdb[4YKD] SKIPPED (not running tests r...) [ 65%] tests/core_test.py::test_long_pdb[1NH9] SKIPPED (not running tests r...) [ 65%] tests/core_test.py::test_long_pdb[4L9E] SKIPPED (not running tests r...) [ 65%] tests/core_test.py::test_long_pdb[3CSR] SKIPPED (not running tests r...) [ 66%] 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 [ 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 [ 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 [ 67%] tests/core_test.py::test_broken_backbone[2V75] -------------------------------- live log call --------------------------------- INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder2/pytest-0/test_broken_backbone_2V75_0/2V75.log INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. INFO PDB2PQR3.6.1:main.py:763 Loading topology files. INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 XFAIL [ 67%] tests/core_test.py::test_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/dx2cube.pqr] PASSED [ 68%] tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 68%] tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 68%] 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_whitespace_ff=TYL06.pqr] PASSED [ 69%] tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 69%] 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/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 70%] tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 70%] tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 71%] tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 71%] tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 71%] tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 72%] tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 72%] tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 72%] tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 73%] tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 73%] tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 73%] tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 74%] tests/io_test.py::test_read_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 59.19s ================== 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 /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) 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/lib/python3.12/dist-packages creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/.pytest_cache creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/.pytest_cache/v creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/.pytest_cache/v/cache/stepwise -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/.pytest_cache/v/cache/nodeids -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/.pytest_cache/CACHEDIR.TAG -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/.pytest_cache copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/.pytest_cache/.gitignore -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/.pytest_cache copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/.pytest_cache/README.md -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/.pytest_cache creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/na.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/biomolecule.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/forcefield.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/cells.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/definitions.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/cif.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/inputgen.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/psize.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/io.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/debump.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/quatfit.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/utilities.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/_version.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/config.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/structures.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/pdb.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/residue.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/aa.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/main.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__pycache__ creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/TYL06.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/SWANSON.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/PEOEPB.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/PARSE.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/CHARMM.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/AMBER.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/TYL06.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/SWANSON.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/PEOEPB.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/PARSE.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/CHARMM.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/AMBER.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/TOPOLOGY.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/PATCHES.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/NA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/HYDROGENS.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/dat/AA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/dat creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/ligand creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/ligand/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/ligand/__pycache__/peoe.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/ligand/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/ligand/__pycache__/mol2.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/ligand/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/ligand/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/ligand/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/ligand/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/ligand copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/ligand/peoe.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/ligand copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/ligand/mol2.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/ligand copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/ligand/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/ligand creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/hydrogens creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/hydrogens/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/hydrogens/__pycache__/optimize.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/hydrogens/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/hydrogens/__pycache__/structures.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/hydrogens/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/hydrogens/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/hydrogens/__pycache__ copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/hydrogens/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/hydrogens copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/hydrogens/optimize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/hydrogens copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/hydrogens/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/hydrogens copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/utilities.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/run.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/residue.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/quatfit.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/psize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/pdb.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/na.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/main.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/io.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/inputgen.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/forcefield.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/definitions.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/debump.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/config.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/cif.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/cells.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/biomolecule.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/aa.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/_version.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__main__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.12/build/pdb2pqr/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/ligand/topology.py to topology.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/ligand/peoe.py to peoe.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/ligand/mol2.py to mol2.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/ligand/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/hydrogens/structures.py to structures.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/hydrogens/optimize.py to optimize.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/hydrogens/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/utilities.py to utilities.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/topology.py to topology.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/structures.py to structures.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/run.py to run.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/residue.py to residue.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/quatfit.py to quatfit.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/psize.py to psize.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/pdb.py to pdb.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/na.py to na.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/main.py to main.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/io.py to io.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/inputgen.py to inputgen.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/forcefield.py to forcefield.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/definitions.py to definitions.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/debump.py to debump.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/config.py to config.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/cif.py to cif.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/cells.py to cells.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/biomolecule.py to biomolecule.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/aa.py to aa.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/_version.py to _version.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__main__.py to __main__.cpython-312.pyc byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.12/dist-packages/pdb2pqr/__init__.py to __init__.cpython-312.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/python3.12/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-doc' in '../pdb2pqr-doc_3.6.1+dfsg-1_all.deb'. dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_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_arm64.buildinfo dpkg-genchanges --build=binary -O../pdb2pqr_3.6.1+dfsg-1_arm64.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/5800/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/5800/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/5800 and its subdirectories I: Current time: Wed Nov 13 09:45:21 +14 2024 I: pbuilder-time-stamp: 1731440721