Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/pdb2pqr/pdb2pqr_2.1.1+dfsg-7_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/pdb2pqr-2.1.1+dfsg-72g3qegmn/pdb2pqr_2.1.1+dfsg-7_all.buildinfo Get source package info: pdb2pqr=2.1.1+dfsg-7 Source URL: http://snapshot.notset.fr/mr/package/pdb2pqr/2.1.1+dfsg-7/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.1-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-6 binutils=2.34-5 binutils-common=2.34-5 binutils-x86-64-linux-gnu=2.34-5 bsdmainutils=11.1.2+b1 bsdutils=1:2.34-0.1 build-essential=12.8 bzip2=1.0.8-2 coreutils=8.30-3+b1 cpp=4:9.2.1-3.1 cpp-9=9.3.0-8 dash=0.5.10.2-6 debconf=1.5.73 debhelper=12.10 debianutils=4.9.1 dh-autoreconf=19 dh-python=4.20200315 dh-strip-nondeterminism=1.6.3-2 diffutils=1:3.7-3 docbook-xml=4.5-9 docbook-xsl=1.79.1+dfsg-2 dos2unix=7.4.0-2 dpkg=1.19.7 dpkg-dev=1.19.7 dwz=0.13-5 fdisk=2.34-0.1 file=1:5.38-4 findutils=4.7.0-1 fontconfig-config=2.13.1-3 fonts-dejavu-core=2.37-1 g++=4:9.2.1-3.1 g++-9=9.3.0-8 gcc=4:9.2.1-3.1 gcc-10-base=10-20200324-1 gcc-9=9.3.0-8 gcc-9-base=9.3.0-8 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 gfortran=4:9.2.1-3.1 gfortran-9=9.3.0-8 grep=3.4-1 groff-base=1.22.4-4 gzip=1.10-2 hostname=3.23 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-6 libarchive-zip-perl=1.68-1 libasan5=9.3.0-8 libatomic1=10-20200324-1 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-2 libaudit1=1:2.8.5-2+b1 libbinutils=2.34-5 libblas3=3.9.0-1 libblkid1=2.34-0.1 libboost-iostreams1.67.0=1.67.0-17 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-2 libc-bin=2.30-4 libc-dev-bin=2.30-4 libc6=2.30-4 libc6-dev=2.30-4 libcairo2=1.16.0-4 libcap-ng0=0.7.9-2.1+b2 libcc1-0=10-20200324-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.15-1 libcrypt1=1:4.4.15-1 libctf-nobfd0=2.34-5 libctf0=2.34-5 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.251 libdebhelper-perl=12.10 libdpkg-perl=1.19.7 libelf1=0.176-1.1 libexpat1=2.2.9-1 libexpat1-dev=2.2.9-1 libfdisk1=2.34-0.1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.6.3-2 libfontconfig1=2.13.1-3 libfreetype6=2.10.1-2 libgcc-9-dev=9.3.0-8 libgcc-s1=10-20200324-1 libgcrypt20=1.8.5-5 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libgfortran-9-dev=9.3.0-8 libgfortran5=10-20200324-1 libglib2.0-0=2.64.1-1 libgmp10=2:6.2.0+dfsg-4 libgomp1=10-20200324-1 libgpg-error0=1.37-1 libicu63=63.2-3 libisl22=0.22.1-1 libitm1=10-20200324-1 liblapack3=3.9.0-1 liblsan0=10-20200324-1 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-4 libmagic1=1:5.38-4 libmount1=2.34-0.1 libmpc3=1.1.0-1 libmpdec2=2.4.2-3 libmpfr6=4.0.2-1 libncursesw6=6.2-1 libopenbabel6=3.0.0+dfsg-3+b1 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-12+b1 libperl5.30=5.30.0-9 libpipeline1=1.5.2-2 libpixman-1-0=0.36.0-1 libpng16-16=1.6.37-2 libpython3-dev=3.8.2-2 libpython3-stdlib=3.8.2-2 libpython3.7-minimal=3.7.7-1 libpython3.7-stdlib=3.7.7-1 libpython3.8=3.8.2-1 libpython3.8-dev=3.8.2-1 libpython3.8-minimal=3.8.2-1 libpython3.8-stdlib=3.8.2-1 libquadmath0=10-20200324-1 libreadline8=8.0-4 libschroedinger-maeparser1=1.2.2-1 libseccomp2=2.4.3-1 libselinux1=3.0-1+b2 libsigsegv2=2.12-2 libsmartcols1=2.34-0.1 libsqlite3-0=3.31.1-4 libssl1.1=1.1.1e-1 libstdc++-9-dev=9.3.0-8 libstdc++6=10-20200324-1 libsub-override-perl=0.09-2 libsystemd0=245.2-1 libtinfo6=6.2-1 libtool=2.4.6-14 libtsan0=10-20200324-1 libubsan1=10-20200324-1 libuchardet0=0.0.6-3 libudev1=245.2-1 libunistring2=0.9.10-2 libuuid1=2.34-0.1 libx11-6=2:1.6.9-2 libx11-data=2:1.6.9-2 libxau6=1:1.0.8-1+b2 libxcb-render0=1.14-2 libxcb-shm0=1.14-2 libxcb1=1.14-2 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1+b2 libxml2=2.9.10+dfsg-4 libxml2-utils=2.9.10+dfsg-4 libxrender1=1:0.9.10-1 libxslt1.1=1.1.34-4 linux-libc-dev=5.4.19-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.2.1-1.2 man-db=2.9.1-1 mawk=1.3.4.20200120-2 mime-support=3.64 ncurses-base=6.2-1 ncurses-bin=6.2-1 openbabel=3.0.0+dfsg-3+b1 patch=2.7.6-6 perl=5.30.0-9 perl-base=5.30.0-9 perl-modules-5.30=5.30.0-9 pkg-config=0.29-6 po-debconf=1.0.21 python3=3.8.2-2 python3-dev=3.8.2-2 python3-distutils=3.8.2-2 python3-lib2to3=3.8.2-2 python3-minimal=3.8.2-2 python3-numpy=1:1.17.4-5 python3-pkg-resources=44.0.0-1 python3.7=3.7.7-1 python3.7-minimal=3.7.7-1 python3.8=3.8.2-1 python3.8-dev=3.8.2-1 python3.8-minimal=3.8.2-1 readline-common=8.0-4 scons=3.1.2-2 sed=4.7-1 sensible-utils=0.0.12+nmu1 sgml-base=1.29.1 sgml-data=2.0.11 swig=4.0.1-5 swig4.0=4.0.1-5 sysvinit-utils=2.96-3 tar=1.30+dfsg-7 ucf=3.0038+nmu1 util-linux=2.34-0.1 xml-core=0.18+nmu1 xmlto=0.0.28-2.1 xsltproc=1.1.34-4 xz-utils=5.2.4-1+b1 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200328T093221Z/ 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=2.1.1+dfsg-7 && mkdir -p /build/pdb2pqr-BOUT2F && dpkg-source --no-check -x /*.dsc /build/pdb2pqr-BOUT2F/pdb2pqr-2.1.1+dfsg && chown -R builduser:builduser /build/pdb2pqr-BOUT2F" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/pdb2pqr-BOUT2F/pdb2pqr-2.1.1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1585497829" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/pdb2pqr-BOUT2F /tmp/pdb2pqr-2.1.1+dfsg-72g3qegmn bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200328T093221Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.ExigjuG7Tr 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.ExigjuG7Tr Reading package lists... Building dependency tree... util-linux is already the newest version (2.34-0.1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20200328T093221Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200328T093221Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (663 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 ... 4506 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.30-4) ... 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200328T093221Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.ExigjuG7Tr Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20200328T093221Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 21s (1090 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.ExigjuG7Tr I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d pdb2pqr=2.1.1+dfsg-7 && mkdir -p /build/pdb2pqr-BOUT2F && dpkg-source --no-check -x /*.dsc /build/pdb2pqr-BOUT2F/pdb2pqr-2.1.1+dfsg && chown -R builduser:builduser /build/pdb2pqr-BOUT2F"' exec /tmp/mmdebstrap.ExigjuG7Tr 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 5261 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main pdb2pqr 2.1.1+dfsg-7 (dsc) [2310 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main pdb2pqr 2.1.1+dfsg-7 (tar) [5191 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main pdb2pqr 2.1.1+dfsg-7 (diff) [67.5 kB] Fetched 5261 kB in 4s (1216 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'pdb2pqr_2.1.1+dfsg-7.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting pdb2pqr in /build/pdb2pqr-BOUT2F/pdb2pqr-2.1.1+dfsg dpkg-source: info: unpacking pdb2pqr_2.1.1+dfsg.orig.tar.xz dpkg-source: info: unpacking pdb2pqr_2.1.1+dfsg-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-hashbangs.patch dpkg-source: info: applying no_privacy_breach_logo.patch dpkg-source: info: applying do_not_try_to_build_removed_js_target.patch dpkg-source: info: applying fix_hardening_no_relro dpkg-source: info: applying fix_no_debug_symbols_warning dpkg-source: info: applying spelling.patch dpkg-source: info: applying python3_PR516.patch dpkg-source: info: applying python3_scons.patch dpkg-source: info: applying python3_sundry.patch dpkg-source: info: applying python3_scriptbang.patch dpkg-source: info: applying use_pkg-config.patch dpkg-source: info: applying reproducible-build.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/pdb2pqr-BOUT2F/pdb2pqr-2.1.1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1585497829" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.ExigjuG7Tr dpkg-buildpackage: info: source package pdb2pqr dpkg-buildpackage: info: source version 2.1.1+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pdb2pqr-BOUT2F/pdb2pqr-2.1.1+dfsg' ( cd pdb2pka && \ if [ -e pMC_mult_wrap.cpp.saved ]; then mv pMC_mult_wrap.cpp.saved pMC_mult_wrap.cpp; fi && \ if [ -e pMC_mult.py.saved ]; then mv pMC_mult.py.saved pMC_mult.py; fi ) find . -name *.pyc -delete find . -name *.so -delete find . -name *.os -delete rm -f *.cgi .sconsign.dblite .variables.cache pdb2pqr.py html/server.html src/aconf.py dh_auto_clean make[1]: Leaving directory '/build/pdb2pqr-BOUT2F/pdb2pqr-2.1.1+dfsg' dh_clean debian/rules binary-indep dh binary-indep --with python3 dh_update_autotools_config -i dh_autoreconf -i debian/rules override_dh_auto_configure make[1]: Entering directory '/build/pdb2pqr-BOUT2F/pdb2pqr-2.1.1+dfsg' dh_auto_configure ( cd pdb2pka && \ cp -a pMC_mult_wrap.cpp pMC_mult_wrap.cpp.saved && \ cp -a pMC_mult.py pMC_mult.py.saved && \ swig -c++ -python -o pMC_mult_wrap.cpp pMC_mult.i ) scons \ URL="http://localhost/pdb2pqr/" \ PREFIX="/usr/share/pdb2pqr" scons: Reading SConscript files ... not using opal scons: done reading SConscript files. scons: Building targets ... CopySubAction("pdb2pqr.py", "pdb2pqr.py.in") Chmod("pdb2pqr.py", 0755) CopySubAction("apbs_cgi.cgi", "apbs_cgi.py") Chmod("apbs_cgi.cgi", 0755) CopySubAction("visualize.cgi", "visualize.py") Chmod("visualize.cgi", 0755) CopySubAction("querystatus.cgi", "querystatus.py") Chmod("querystatus.cgi", 0755) CopySubAction("src/aconf.py", "src/aconf.py.in") CopySubAction("html/server.html", "html/server.html.in") Copy("pdb2pqr.cgi", "pdb2pqr.py") g++ -o pdb2pka/substruct/Algorithms.os -c -g -fPIC -I/usr/include/python3.8 -I/usr/include/x86_64-linux-gnu/python3.8 -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include pdb2pka/substruct/Algorithms.cpp In file included from /usr/include/python3.8/numpy/ndarraytypes.h:1830, from /usr/include/python3.8/numpy/ndarrayobject.h:12, from /usr/include/python3.8/numpy/arrayobject.h:4, from pdb2pka/substruct/Algorithms.cpp:43: /usr/include/python3.8/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ pdb2pka/substruct/Algorithms.cpp: In function 'PyObject* initAlgorithms()': pdb2pka/substruct/Algorithms.cpp:333:1: warning: control reaches end of non-void function [-Wreturn-type] 333 | }; | ^ g++ -o pdb2pka/substruct/Algorithms.cpython-38-x86_64-linux-gnu.so -Wl,-z,relro -Wl,-z,now -shared pdb2pka/substruct/Algorithms.os -L/usr/lib g++ -o pdb2pka/pMC_mult.os -c -g -fPIC -I/usr/include/python3.8 -I/usr/include/x86_64-linux-gnu/python3.8 -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include pdb2pka/pMC_mult.cpp g++ -o pdb2pka/pMC_mult_wrap.os -c -g -fPIC -I/usr/include/python3.8 -I/usr/include/x86_64-linux-gnu/python3.8 -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include pdb2pka/pMC_mult_wrap.cpp g++ -o pdb2pka/_pMC_mult.cpython-38-x86_64-linux-gnu.so -Wl,-z,relro -Wl,-z,now -shared pdb2pka/pMC_mult.os pdb2pka/pMC_mult_wrap.os -L/usr/lib scons: done building targets. TARGETS: ['pdb2pqr.py', 'apbs_cgi.cgi', 'visualize.cgi', 'querystatus.cgi', 'src/aconf.py', 'html/server.html', 'pdb2pqr.cgi', 'pdb2pka/substruct/Algorithms.cpython-38-x86_64-linux-gnu.so', 'pdb2pka/_pMC_mult.cpython-38-x86_64-linux-gnu.so'] ======================== Configuration Parameters ======================== Version: 2.1.1 Install directory: /usr/share/pdb2pqr/ pdb2pka and ligand support: True Path to the website directory: http://localhost/pdb2pqr/ PDB2PQR jobs run via the web interface will be forked on the server. The preferred way to configure the build is by editing the file build_config.py Run scons with the python3 that you intend to use with pdb2pqr. For example: "scons" will setup pdb2pqr to be run with Debian default Python3 interpreter Run "scons install" to install pdb2pqr in /usr/share/pdb2pqr/ Run "scons basic-test" for a basic functionality test Run "scons advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled. Run "scons complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled. Run "scons pdb2pka-test" for a test of PDB2PKA functionality. Requires numpy, PDB2PKA support compiled AND the APBS python3 libraries compiled and installed in the pdb2pka directory. To setup a web service create a symbolic link to /usr/share/pdb2pqr/ that enables you to view http://localhost/pdb2pqr/ after running "scons install" Run "scons msvs" to build Visual Studio projects for the Algorithms and pMC_mult modules. VS project generation is not well supported in scons. Resulting projects should build using NMAKE but cannot be used for debugging. The resulting projects will need to modified to use VS natively to compile the code or debug. Build succeeded. make[1]: Leaving directory '/build/pdb2pqr-BOUT2F/pdb2pqr-2.1.1+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -i dh_prep -i dh_install -i dh_installdocs -i debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/pdb2pqr-BOUT2F/pdb2pqr-2.1.1+dfsg' dh_installchangelogs ChangeLog.md make[1]: Leaving directory '/build/pdb2pqr-BOUT2F/pdb2pqr-2.1.1+dfsg' debian/rules override_dh_installexamples make[1]: Entering directory '/build/pdb2pqr-BOUT2F/pdb2pqr-2.1.1+dfsg' dh_installexamples for bakerdoc in $( grep -l "http://agave.wustl.edu/css/baker.css" -R debian/pdb2pqr-doc/usr/share/doc/pdb2pqr/* ); do \ sed "s|href=\"http://agave.wustl.edu/css/baker.css\"|href=\"baker.css\"|g" -i $bakerdoc; done make[1]: Leaving directory '/build/pdb2pqr-BOUT2F/pdb2pqr-2.1.1+dfsg' dh_python3 -i E: dh_python3 dh_python3:176: no package to act on (python3-foo or one with ${python3:Depends} in Depends) dh_perl -i dh_link -i dh_strip_nondeterminism -i dh_compress -i dh_fixperms -i dh_missing -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'pdb2pqr-doc' in '../pdb2pqr-doc_2.1.1+dfsg-7_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../pdb2pqr_2.1.1+dfsg-7_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-BOUT2F /tmp/pdb2pqr-2.1.1+dfsg-72g3qegmn I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.ExigjuG7Tr... I: success in 479.5104 seconds md5: pdb2pqr-doc_2.1.1+dfsg-7_all.deb: OK sha1: pdb2pqr-doc_2.1.1+dfsg-7_all.deb: OK sha256: pdb2pqr-doc_2.1.1+dfsg-7_all.deb: OK Checksums: OK