Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/pdb2pqr/pdb2pqr_3.5.2+dfsg-2_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/pdb2pqr-3.5.2+dfsg-24ndpb2bb/pdb2pqr_3.5.2+dfsg-2_all.buildinfo Get source package info: pdb2pqr=3.5.2+dfsg-2 Source URL: http://snapshot.notset.fr/mr/package/pdb2pqr/3.5.2+dfsg-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 binutils=2.38-3 binutils-common=2.38-3 binutils-x86-64-linux-gnu=2.38-3 bsdextrautils=2.37.3-1+b1 bsdutils=1:2.37.3-1+b1 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-18 dash=0.5.11+git20210903+057cd650a4ed-7 debconf=1.5.79 debhelper=13.6 debianutils=5.7-0.1 dh-autoreconf=20 dh-python=5.20220215 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 docutils-common=0.17.1+dfsg-2 dpkg=1.21.1 dpkg-dev=1.21.1 dwz=0.14-1 file=1:5.41-2 findutils=4.9.0-2 fonts-font-awesome=5.0.10+really4.7.0~dfsg-4.1 fonts-lato=2.0-2.1 g++=4:11.2.0-2 g++-11=11.2.0-18 gcc=4:11.2.0-2 gcc-11=11.2.0-18 gcc-11-base=11.2.0-18 gcc-12-base=12-20220302-1 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-8 gzip=1.10-4 help2man=1.49.1 hostname=3.23 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-18 libatomic1=12-20220302-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbinutils=2.38-3 libblas3=3.10.0-2 libblkid1=2.37.3-1+b1 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=12-20220302-1 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-3 libctf0=2.38-3 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.6 libdpkg-perl=1.21.1 libelf1=0.186-1 libexpat1=2.4.7-1 libexpat1-dev=2.4.7-1 libffi8=3.4.2-4 libfile-stripnondeterminism-perl=1.13.0-1 libgcc-11-dev=11.2.0-18 libgcc-s1=12-20220302-1 libgcrypt20=1.9.4-5 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgfortran5=12-20220302-1 libgmp10=2:6.2.1+dfsg-3 libgomp1=12-20220302-1 libgpg-error0=1.43-3 libgssapi-krb5-2=1.19.2-2+b1 libicu67=67.1-7 libisl23=0.24-2 libitm1=12-20220302-1 libjs-jquery=3.6.0+dfsg+~3.5.13-1 libjs-sphinxdoc=4.3.2-1 libjs-underscore=1.13.2~dfsg-2 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 liblapack3=3.10.0-2 liblocale-gettext-perl=1.07-4+b2 liblsan0=12-20220302-1 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmount1=2.37.3-1+b1 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncursesw6=6.3-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.34=5.34.0-3 libpipeline1=1.5.5-1 libpython3-dev=3.9.8-1 libpython3-stdlib=3.9.8-1 libpython3.10-minimal=3.10.2-6 libpython3.10-stdlib=3.10.2-6 libpython3.9=3.9.10-2 libpython3.9-dev=3.9.10-2 libpython3.9-minimal=3.9.10-2 libpython3.9-stdlib=3.9.10-2 libquadmath0=12-20220302-1 libreadline8=8.1.2-1 libseccomp2=2.5.3-2 libselinux1=3.3-1+b2 libsigsegv2=2.14-1 libsmartcols1=2.37.3-1+b1 libsqlite3-0=3.38.1-1 libssl1.1=1.1.1m-1 libstdc++-11-dev=11.2.0-18 libstdc++6=12-20220302-1 libsub-override-perl=0.09-2 libsystemd0=250.3-2 libtinfo6=6.3-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-18 libubsan1=12-20220302-1 libuchardet0=0.0.7-1 libudev1=250.3-2 libunistring2=1.0-1 libuuid1=2.37.3-1+b1 libxml2=2.9.13+dfsg-1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.16.12-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.1-1 mawk=1.3.4.20200120-3+b1 media-types=6.0.0 ncurses-base=6.3-2 ncurses-bin=6.3-2 openssl=1.1.1m-1 patch=2.7.6-7 perl=5.34.0-3 perl-base=5.34.0-3 perl-modules-5.34=5.34.0-3 po-debconf=1.0.21+nmu1 python-babel-localedata=2.8.0+dfsg.1-7 python3=3.9.8-1 python3-alabaster=0.7.12-1 python3-attr=21.2.0-1 python3-babel=2.8.0+dfsg.1-7 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-1 python3-dateutil=2.8.1-6 python3-dev=3.9.8-1 python3-distutils=3.9.10-1 python3-docutils=0.17.1+dfsg-2 python3-idna=3.3-1 python3-imagesize=1.3.0-1 python3-importlib-metadata=4.6.4-1 python3-iniconfig=1.1.1-2 python3-jinja2=3.0.3-1 python3-lib2to3=3.9.10-1 python3-markupsafe=2.0.1-2+b1 python3-minimal=3.9.8-1 python3-more-itertools=8.10.0-2 python3-numpy=1:1.21.5-1 python3-packaging=21.3-1 python3-pandas=1.3.5+dfsg-3 python3-pandas-lib=1.3.5+dfsg-3 python3-pdbx=2.0.1-2 python3-pkg-resources=59.6.0-1.2 python3-pluggy=0.13.0-7.1 python3-propka=3.4.0-3 python3-py=1.10.0-1 python3-pygments=2.11.2+dfsg-2 python3-pyparsing=3.0.7-1 python3-pytest=6.2.5-1 python3-requests=2.25.1+dfsg-2 python3-roman=3.3-1 python3-setuptools=59.6.0-1.2 python3-six=1.16.0-3 python3-snowballstemmer=2.2.0-1 python3-sphinx=4.3.2-1 python3-sphinx-rtd-theme=1.0.0+dfsg-1 python3-testfixtures=6.18.3-2 python3-toml=0.10.2-1 python3-tz=2021.3-1 python3-urllib3=1.26.8-1 python3-zipp=1.0.0-3 python3.10=3.10.2-6 python3.10-minimal=3.10.2-6 python3.9=3.9.10-2 python3.9-dev=3.9.10-2 python3.9-minimal=3.9.10-2 readline-common=8.1.2-1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sgml-base=1.30 sphinx-common=4.3.2-1 sphinx-rtd-theme-common=1.0.0+dfsg-1 sysvinit-utils=3.01-1 tar=1.34+dfsg-1 tzdata=2021e-1 util-linux=2.37.3-1+b1 xml-core=0.18+nmu1 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220316T034435Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220316T034435Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220319T033210Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220313T210822Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d pdb2pqr=3.5.2+dfsg-2 && mkdir -p /build/pdb2pqr-HwKjfM && dpkg-source --no-check -x /*.dsc /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg && chown -R builduser:builduser /build/pdb2pqr-HwKjfM" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1647235678" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/pdb2pqr-HwKjfM /tmp/pdb2pqr-3.5.2+dfsg-24ndpb2bb bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220313T210822Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.9WY0DVohrA as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.9WY0DVohrA Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.3-1+b1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220313T210822Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220313T210822Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (880 kB/s) Selecting previously unselected package libfakeroot:amd64. (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 ... 4696 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220316T034435Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220316T034435Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220319T033210Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220313T210822Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.9WY0DVohrA Get:1 http://snapshot.notset.fr/archive/debian/20220316T034435Z bookworm InRelease [130 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220319T033210Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20220313T210822Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20220316T034435Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220316T034435Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220316T034435Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220316T034435Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220316T034435Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220316T034435Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20220316T034435Z bookworm/main Sources [11.9 MB] Get:5 http://snapshot.notset.fr/archive/debian/20220316T034435Z bookworm/main amd64 Packages [11.3 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220319T033210Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220319T033210Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220319T033210Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220319T033210Z unstable/main amd64 Packages [12.3 MB] Fetched 35.9 MB in 29s (1241 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.9WY0DVohrA I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d pdb2pqr=3.5.2+dfsg-2 && mkdir -p /build/pdb2pqr-HwKjfM && dpkg-source --no-check -x /*.dsc /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg && chown -R builduser:builduser /build/pdb2pqr-HwKjfM"' exec /tmp/mmdebstrap.9WY0DVohrA Reading package lists... NOTICE: 'pdb2pqr' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/pdb2pqr.git Please use: git clone https://salsa.debian.org/med-team/pdb2pqr.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 7606 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220316T034435Z bookworm/main pdb2pqr 3.5.2+dfsg-2 (dsc) [2490 B] Get:2 http://snapshot.notset.fr/archive/debian/20220316T034435Z bookworm/main pdb2pqr 3.5.2+dfsg-2 (tar) [7594 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220316T034435Z bookworm/main pdb2pqr 3.5.2+dfsg-2 (diff) [9600 B] Fetched 7606 kB in 6s (1275 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'pdb2pqr_3.5.2+dfsg-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting pdb2pqr in /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg dpkg-source: info: unpacking pdb2pqr_3.5.2+dfsg.orig.tar.xz dpkg-source: info: unpacking pdb2pqr_3.5.2+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip-network-tests.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1647235678" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.9WY0DVohrA dpkg-buildpackage: info: source package pdb2pqr dpkg-buildpackage: info: source version 3.5.2+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . debian/rules clean dh clean --buildsystem pybuild --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg' dh_auto_clean I: pybuild base:237: python3.9 setup.py clean running clean removing '/build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it rm -rf pdb2pqr.egg-info make[1]: Leaving directory '/build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-indep dh binary-indep --buildsystem pybuild --with python3 dh_update_autotools_config -i -O--buildsystem=pybuild dh_autoreconf -i -O--buildsystem=pybuild dh_auto_configure -i -O--buildsystem=pybuild I: pybuild base:237: python3.9 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg' dh_auto_build I: pybuild base:237: /usr/bin/python3 setup.py build running build running build_py creating /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/__init__.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/__main__.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/_version.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/aa.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/biomolecule.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/cells.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/cif.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/config.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/debump.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/definitions.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/forcefield.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/inputgen.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/io.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/main.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/na.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/pdb.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/psize.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/quatfit.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/residue.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/run.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/structures.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/topology.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr copying pdb2pqr/utilities.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr creating /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/hydrogens copying pdb2pqr/hydrogens/__init__.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/hydrogens copying pdb2pqr/hydrogens/optimize.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/hydrogens copying pdb2pqr/hydrogens/structures.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/hydrogens creating /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/ligand copying pdb2pqr/ligand/__init__.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/ligand copying pdb2pqr/ligand/mol2.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/ligand copying pdb2pqr/ligand/peoe.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/ligand copying pdb2pqr/ligand/topology.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/ligand creating /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/AA.xml -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/HYDROGENS.xml -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/NA.xml -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/PATCHES.xml -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/TOPOLOGY.xml -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/AMBER.DAT -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/CHARMM.DAT -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/PARSE.DAT -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/PEOEPB.DAT -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/SWANSON.DAT -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/TYL06.DAT -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/AMBER.names -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/CHARMM.names -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/PARSE.names -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/PEOEPB.names -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/SWANSON.names -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat copying pdb2pqr/dat/TYL06.names -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat PYTHONPATH=. python3 -m sphinx -N -bhtml docs/source build/html Running Sphinx v4.3.2 making output directory... done WARNING: html_static_path entry '_static' does not exist loading intersphinx inventory from https://docs.python.org/3/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : Proxy URL had no scheme, should start with http:// or https:// [autosummary] generating autosummary for: api/aa.rst, api/biomolecule.rst, api/cells.rst, api/cif.rst, api/config.rst, api/debump.rst, api/definitions.rst, api/forcefield.rst, api/hydrogens.rst, api/index.rst, ..., formats/xml-names.rst, getting.rst, help.rst, index.rst, releases.rst, supporting.rst, using/algorithms.rst, using/examples.rst, using/index.rst, using/other-software.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 39 source files that are out of date updating environment: [new config] 39 added, 0 changed, 0 removed reading sources... [ 2%] api/aa reading sources... [ 5%] api/biomolecule reading sources... [ 7%] api/cells reading sources... [ 10%] api/cif reading sources... [ 12%] api/config reading sources... [ 15%] api/debump reading sources... [ 17%] api/definitions reading sources... [ 20%] api/forcefield reading sources... [ 23%] api/hydrogens reading sources... [ 25%] api/index reading sources... [ 28%] api/inputgen reading sources... [ 30%] api/io reading sources... [ 33%] api/ligand reading sources... [ 35%] api/main reading sources... [ 38%] api/na reading sources... [ 41%] api/pdb reading sources... [ 43%] api/psize reading sources... [ 46%] api/quatfit reading sources... [ 48%] api/residue reading sources... [ 51%] api/run reading sources... [ 53%] api/structures reading sources... [ 56%] api/topology reading sources... [ 58%] api/utilities reading sources... [ 61%] extending reading sources... [ 64%] formats/dat reading sources... [ 66%] formats/index reading sources... [ 69%] formats/mol2 reading sources... [ 71%] formats/pdb reading sources... [ 74%] formats/pqr reading sources... [ 76%] formats/xml-names reading sources... [ 79%] getting reading sources... [ 82%] help reading sources... [ 84%] index reading sources... [ 87%] releases reading sources... [ 89%] supporting reading sources... [ 92%] using/algorithms reading sources... [ 94%] using/examples reading sources... [ 97%] using/index reading sources... [100%] using/other-software looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 2%] api/aa writing output... [ 5%] api/biomolecule writing output... [ 7%] api/cells writing output... [ 10%] api/cif writing output... [ 12%] api/config writing output... [ 15%] api/debump writing output... [ 17%] api/definitions writing output... [ 20%] api/forcefield writing output... [ 23%] api/hydrogens writing output... [ 25%] api/index writing output... [ 28%] api/inputgen writing output... [ 30%] api/io writing output... [ 33%] api/ligand writing output... [ 35%] api/main writing output... [ 38%] api/na writing output... [ 41%] api/pdb writing output... [ 43%] api/psize writing output... [ 46%] api/quatfit writing output... [ 48%] api/residue writing output... [ 51%] api/run writing output... [ 53%] api/structures writing output... [ 56%] api/topology writing output... [ 58%] api/utilities writing output... [ 61%] extending writing output... [ 64%] formats/dat writing output... [ 66%] formats/index writing output... [ 69%] formats/mol2 writing output... [ 71%] formats/pdb writing output... [ 74%] formats/pqr writing output... [ 76%] formats/xml-names writing output... [ 79%] getting writing output... [ 82%] help writing output... [ 84%] index writing output... [ 87%] releases writing output... [ 89%] supporting writing output... [ 92%] using/algorithms writing output... [ 94%] using/examples writing output... [ 97%] using/index writing output... [100%] using/other-software generating indices... genindex py-modindex done highlighting module code... [ 4%] pdb2pqr.aa highlighting module code... [ 8%] pdb2pqr.biomolecule highlighting module code... [ 12%] pdb2pqr.cells highlighting module code... [ 16%] pdb2pqr.cif highlighting module code... [ 20%] pdb2pqr.debump highlighting module code... [ 24%] pdb2pqr.definitions highlighting module code... [ 28%] pdb2pqr.forcefield highlighting module code... [ 32%] pdb2pqr.hydrogens highlighting module code... [ 36%] pdb2pqr.hydrogens.optimize highlighting module code... [ 40%] pdb2pqr.hydrogens.structures highlighting module code... [ 44%] pdb2pqr.inputgen highlighting module code... [ 48%] pdb2pqr.io highlighting module code... [ 52%] pdb2pqr.ligand.mol2 highlighting module code... [ 56%] pdb2pqr.ligand.peoe highlighting module code... [ 60%] pdb2pqr.ligand.topology highlighting module code... [ 64%] pdb2pqr.main highlighting module code... [ 68%] pdb2pqr.na highlighting module code... [ 72%] pdb2pqr.pdb highlighting module code... [ 76%] pdb2pqr.psize highlighting module code... [ 80%] pdb2pqr.quatfit highlighting module code... [ 84%] pdb2pqr.residue highlighting module code... [ 88%] pdb2pqr.run highlighting module code... [ 92%] pdb2pqr.structures highlighting module code... [ 96%] pdb2pqr.topology highlighting module code... [100%] pdb2pqr.utilities writing additional pages... search done copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 2 warnings. The HTML pages are in build/html. make[1]: Leaving directory '/build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg' dh: command-omitted: The call to "dh_auto_test -i -O--buildsystem=pybuild" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -i -O--buildsystem=pybuild dh_prep -i -O--buildsystem=pybuild dh_installdirs -i -O--buildsystem=pybuild dh_auto_install -i -O--buildsystem=pybuild I: pybuild base:237: /usr/bin/python3 setup.py install --root /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running install_lib creating /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr creating /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib creating /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9 creating /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages creating /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/__init__.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/__main__.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/_version.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/aa.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/biomolecule.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/cells.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/cif.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/config.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/debump.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/definitions.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/forcefield.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/inputgen.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/io.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/main.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/na.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/pdb.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/psize.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/quatfit.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/residue.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/run.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/structures.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/topology.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/utilities.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr creating /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/hydrogens copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/hydrogens/__init__.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/hydrogens copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/hydrogens/optimize.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/hydrogens copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/hydrogens/structures.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/hydrogens creating /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/ligand copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/ligand/__init__.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/ligand copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/ligand/mol2.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/ligand copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/ligand/peoe.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/ligand copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/ligand/topology.py -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/ligand creating /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/AA.xml -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/HYDROGENS.xml -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/NA.xml -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/PATCHES.xml -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/TOPOLOGY.xml -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/AMBER.DAT -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/CHARMM.DAT -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/PARSE.DAT -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/PEOEPB.DAT -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/SWANSON.DAT -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/TYL06.DAT -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/AMBER.names -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/CHARMM.names -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/PARSE.names -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/PEOEPB.names -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/SWANSON.names -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat copying /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/.pybuild/cpython3_3.9/build/pdb2pqr/dat/TYL06.names -> /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/dat byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/__init__.py to __init__.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/__main__.py to __main__.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/_version.py to _version.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/aa.py to aa.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/biomolecule.py to biomolecule.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/cells.py to cells.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/cif.py to cif.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/config.py to config.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/debump.py to debump.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/definitions.py to definitions.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/forcefield.py to forcefield.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/inputgen.py to inputgen.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/io.py to io.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/main.py to main.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/na.py to na.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/pdb.py to pdb.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/psize.py to psize.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/quatfit.py to quatfit.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/residue.py to residue.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/run.py to run.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/structures.py to structures.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/topology.py to topology.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/utilities.py to utilities.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/hydrogens/__init__.py to __init__.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/hydrogens/optimize.py to optimize.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/hydrogens/structures.py to structures.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/ligand/__init__.py to __init__.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/ligand/mol2.py to mol2.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/ligand/peoe.py to peoe.cpython-39.pyc byte-compiling /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr/ligand/topology.py to topology.cpython-39.pyc running install_egg_info running egg_info creating pdb2pqr.egg-info writing pdb2pqr.egg-info/PKG-INFO writing dependency_links to pdb2pqr.egg-info/dependency_links.txt writing entry points to pdb2pqr.egg-info/entry_points.txt writing requirements to pdb2pqr.egg-info/requires.txt writing top-level names to pdb2pqr.egg-info/top_level.txt writing manifest file 'pdb2pqr.egg-info/SOURCES.txt' reading manifest file 'pdb2pqr.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'pdb2pka' adding license file 'LICENSE.md' adding license file 'COPYING' writing manifest file 'pdb2pqr.egg-info/SOURCES.txt' Copying pdb2pqr.egg-info to /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/lib/python3.9/dist-packages/pdb2pqr-3.5.2.egg-info Skipping SOURCES.txt running install_scripts Installing dx2cube script to /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/bin Installing inputgen script to /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/bin Installing pdb2pqr30 script to /build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg/debian/tmp/usr/bin dh_install -i -O--buildsystem=pybuild debian/rules override_dh_installdocs make[1]: Entering directory '/build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg' dh_installdocs dh_installdocs -p pdb2pqr-doc --doc-main-package pdb2pqr build/html make[1]: Leaving directory '/build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg' dh_sphinxdoc -i -O--buildsystem=pybuild dh_installchangelogs -i -O--buildsystem=pybuild dh_installexamples -i -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg' PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/dx2cube --no-info --version-string 3.5.2+dfsg > dx2cube.1 PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/inputgen --no-info --version-string 3.5.2+dfsg > inputgen.1 PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/pdb2pqr30 --no-info --version-string 3.5.2+dfsg > pdb2pqr30.1 dh_installman make[1]: Leaving directory '/build/pdb2pqr-HwKjfM/pdb2pqr-3.5.2+dfsg' dh_python3 -i -O--buildsystem=pybuild dh_installsystemduser -i -O--buildsystem=pybuild dh_perl -i -O--buildsystem=pybuild dh_link -i -O--buildsystem=pybuild dh_strip_nondeterminism -i -O--buildsystem=pybuild dh_compress -i -O--buildsystem=pybuild dh_fixperms -i -O--buildsystem=pybuild dh_missing -i -O--buildsystem=pybuild dh_installdeb -i -O--buildsystem=pybuild dh_gencontrol -i -O--buildsystem=pybuild dpkg-gencontrol: warning: package pdb2pqr-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -i -O--buildsystem=pybuild dh_builddeb -i -O--buildsystem=pybuild dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_3.5.2+dfsg-2_all.deb'. dpkg-deb: building package 'python3-pdb2pqr' in '../python3-pdb2pqr_3.5.2+dfsg-2_all.deb'. dpkg-deb: building package 'pdb2pqr-doc' in '../pdb2pqr-doc_3.5.2+dfsg-2_all.deb'. dpkg-genbuildinfo --build=all -O../pdb2pqr_3.5.2+dfsg-2_all.buildinfo dpkg-genchanges --build=all -O../pdb2pqr_3.5.2+dfsg-2_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/pdb2pqr-HwKjfM /tmp/pdb2pqr-3.5.2+dfsg-24ndpb2bb I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.9WY0DVohrA... I: success in 407.2139 seconds md5: pdb2pqr-doc_3.5.2+dfsg-2_all.deb: OK md5: pdb2pqr_3.5.2+dfsg-2_all.deb: OK md5: python3-pdb2pqr_3.5.2+dfsg-2_all.deb: OK sha1: pdb2pqr-doc_3.5.2+dfsg-2_all.deb: OK sha1: pdb2pqr_3.5.2+dfsg-2_all.deb: OK sha1: python3-pdb2pqr_3.5.2+dfsg-2_all.deb: OK sha256: pdb2pqr-doc_3.5.2+dfsg-2_all.deb: OK sha256: pdb2pqr_3.5.2+dfsg-2_all.deb: OK sha256: python3-pdb2pqr_3.5.2+dfsg-2_all.deb: OK Checksums: OK