Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/pdb2pqr/pdb2pqr_2.1.1+dfsg-7+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/pdb2pqr-2.1.1+dfsg-7+b1qkuf21ag/pdb2pqr_2.1.1+dfsg-7+b1_amd64.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=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc2-1 binutils=2.35.1-3 binutils-common=2.35.1-3 binutils-x86-64-linux-gnu=2.35.1-3 bsdextrautils=2.36.1-1 bsdutils=1:2.36.1-1 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-18 dash=0.5.11+git20200708+dd9ef66-2 debconf=1.5.74 debhelper=13.2.1 debianutils=4.11.2 dh-autoreconf=19 dh-python=4.20201102 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 docbook-xml=4.5-9 docbook-xsl=1.79.2+dfsg-1 dos2unix=7.4.1-1 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.39-3 findutils=4.7.0+git20201010-2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:10.2.0-1 g++-10=10.2.0-18 gcc=4:10.2.0-1 gcc-10=10.2.0-18 gcc-10-base=10.2.0-18 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 gfortran=4:10.2.0-1 gfortran-10=10.2.0-18 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan6=10.2.0-18 libatomic1=10.2.0-18 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1 libbinutils=2.35.1-3 libblas3=3.9.0-3 libblkid1=2.36.1-1 libboost-iostreams1.71.0=1.71.0-7+b1 libbrotli1=1.0.9-2+b1 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-4 libc-dev-bin=2.31-4 libc6=2.31-4 libc6-dev=2.31-4 libcairo2=1.16.0-4 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-18 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-3 libctf0=2.35.1-3 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.2.1 libdpkg-perl=1.20.5 libelf1=0.182-1 libexpat1=2.2.10-1 libexpat1-dev=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.9.0-1 libfontconfig1=2.13.1-4.2 libfreetype6=2.10.2+dfsg-4 libgcc-10-dev=10.2.0-18 libgcc-s1=10.2.0-18 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgfortran-10-dev=10.2.0-18 libgfortran5=10.2.0-18 libglib2.0-0=2.66.3-1 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.0-18 libgpg-error0=1.38-2 libgssapi-krb5-2=1.17-10 libicu67=67.1-4 libinchi1=1.03+dfsg-3 libisl22=0.22.1-1 libitm1=10.2.0-18 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 liblapack3=3.9.0-3 liblsan0=10.2.0-18 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmaeparser1=1.2.4-1 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-1 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncursesw6=6.2+20201114-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnss-nis=3.1-4 libnss-nisplus=1.3-4 libopenbabel7=3.1.1+dfsg-3+b2 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=2:8.39-13 libperl5.32=5.32.0-5 libpipeline1=1.5.3-1 libpixman-1-0=0.36.0-1 libpng16-16=1.6.37-3 libpython3-dev=3.9.0-3 libpython3-stdlib=3.9.0-3 libpython3.8-minimal=3.8.6-1 libpython3.8-stdlib=3.8.6-1 libpython3.9=3.9.0-5 libpython3.9-dev=3.9.0-5 libpython3.9-minimal=3.9.0-5 libpython3.9-stdlib=3.9.0-5 libquadmath0=10.2.0-18 libreadline8=8.1~rc2-2 libseccomp2=2.5.0-3 libselinux1=3.1-2+b1 libsigsegv2=2.12-2 libsmartcols1=2.36.1-1 libsqlite3-0=3.33.0-1 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.0-18 libstdc++6=10.2.0-18 libsub-override-perl=0.09-2 libsystemd0=246.6-3 libtinfo6=6.2+20201114-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.0-18 libubsan1=10.2.0-18 libuchardet0=0.0.7-1 libudev1=246.6-3 libunistring2=0.9.10-4 libuuid1=2.36.1-1 libx11-6=2:1.6.12-1 libx11-data=2:1.6.12-1 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-6.2 libxml2-utils=2.9.10+dfsg-6.2 libxrender1=1:0.9.10-1 libxslt1.1=1.1.34-4 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.6-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 mailcap=3.67 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 media-types=1.0.1 mime-support=3.66 ncurses-base=6.2+20200918-1 ncurses-bin=6.2+20200918-1 openbabel=3.1.1+dfsg-3+b2 patch=2.7.6-6 perl=5.32.0-5 perl-base=5.32.0-5 perl-modules-5.32=5.32.0-5 pkg-config=0.29.2-1 po-debconf=1.0.21 python3=3.9.0-3 python3-dev=3.9.0-3 python3-distutils=3.8.6-1 python3-lib2to3=3.8.6-1 python3-minimal=3.9.0-3 python3-numpy=1:1.19.4-1 python3-pkg-resources=50.3.0-1 python3.8=3.8.6-1 python3.8-minimal=3.8.6-1 python3.9=3.9.0-5 python3.9-dev=3.9.0-5 python3.9-minimal=3.9.0-5 readline-common=8.1~rc2-2 scons=4.0.1+dfsg-2 sed=4.7-1 sensible-utils=0.0.12+nmu1 sgml-base=1.30 sgml-data=2.0.11 swig=4.0.2-1 swig4.0=4.0.2-1 sysvinit-utils=2.96-5 tar=1.30+dfsg-7 ucf=3.0043 util-linux=2.36.1-1 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/20201125T152047Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201119T152556Z/ 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-aZAk4g && dpkg-source --no-check -x /*.dsc /build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg && cd /build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg && { printf '%s' 'pdb2pqr (2.1.1+dfsg-7+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Python 3.9 as default -- amd64 / i386 Build Daemon (x86-csail-01) Fri, 20 Nov 2020 13:01:37 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/pdb2pqr-aZAk4g" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605877297" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/pdb2pqr-aZAk4g /tmp/pdb2pqr-2.1.1+dfsg-7+b1qkuf21ag bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201119T152556Z 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.PqipE9mc63 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.PqipE9mc63 Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201119T152556Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201119T152556Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (904 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 ... 4690 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-4) ... 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/20201125T152047Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201119T152556Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.PqipE9mc63 Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201125T152047Z unstable InRelease [146 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201119T152556Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20201125T152047Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201125T152047Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201125T152047Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201125T152047Z unstable/main amd64 Packages [11.6 MB] Fetched 34.3 MB in 30s (1154 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.PqipE9mc63 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-aZAk4g && dpkg-source --no-check -x /*.dsc /build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg && cd /build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg && { printf '%s' 'pdb2pqr (2.1.1+dfsg-7+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Python 3.9 as default -- amd64 / i386 Build Daemon (x86-csail-01) Fri, 20 Nov 2020 13:01:37 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/pdb2pqr-aZAk4g"' exec /tmp/mmdebstrap.PqipE9mc63 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 5s (1167 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-aZAk4g/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-aZAk4g/pdb2pqr-2.1.1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605877297" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.PqipE9mc63 dpkg-buildpackage: info: source package pdb2pqr dpkg-buildpackage: info: source version 2.1.1+dfsg-7+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-csail-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pdb2pqr-aZAk4g/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-aZAk4g/pdb2pqr-2.1.1+dfsg' dh_clean debian/rules binary-arch dh binary-arch --with python3 dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/pdb2pqr-aZAk4g/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/python3.9 -I/usr/include/x86_64-linux-gnu/python3.9 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include pdb2pka/substruct/Algorithms.cpp In file included from /usr/include/python3.9/numpy/ndarraytypes.h:1822, from /usr/include/python3.9/numpy/ndarrayobject.h:12, from /usr/include/python3.9/numpy/arrayobject.h:4, from pdb2pka/substruct/Algorithms.cpp:43: /usr/include/python3.9/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-39-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/python3.9 -I/usr/include/x86_64-linux-gnu/python3.9 -I/usr/include/python3.9 -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/python3.9 -I/usr/include/x86_64-linux-gnu/python3.9 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include pdb2pka/pMC_mult_wrap.cpp g++ -o pdb2pka/_pMC_mult.cpython-39-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-39-x86_64-linux-gnu.so', 'pdb2pka/_pMC_mult.cpython-39-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-aZAk4g/pdb2pqr-2.1.1+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a dh_installdirs -a debian/rules override_dh_install-arch make[1]: Entering directory '/build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg' dh_install -a dos2unix debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py dos2unix: converting file debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py to Unix format... dos2unix debian/pdb2pqr/usr/share/pdb2pqr/src/psize.py dos2unix: converting file debian/pdb2pqr/usr/share/pdb2pqr/src/psize.py to Unix format... make[1]: Leaving directory '/build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg' dh_installdocs -a debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg' dh_installchangelogs ChangeLog.md make[1]: Leaving directory '/build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg' debian/rules override_dh_installexamples make[1]: Entering directory '/build/pdb2pqr-aZAk4g/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 grep: debian/pdb2pqr-doc/usr/share/doc/pdb2pqr/*: No such file or directory make[1]: Leaving directory '/build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg' debian/rules override_dh_installman-arch make[1]: Entering directory '/build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg' dh_installman -a xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/pdb2pqr.1.xml Note: Writing pdb2pqr.1 xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/psize.1.xml Note: Writing psize.1 xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/propka.1.xml Note: Writing propka.1 make[1]: Leaving directory '/build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg' dh_python3 -a dh_perl -a debian/rules override_dh_link-arch make[1]: Entering directory '/build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg' dh_link -a dh_link -a usr/lib/pdb2pqr/pdb2pka/_pMC_mult.cpython-39-x86_64-linux-gnu.so usr/share/pdb2pqr/pdb2pka/_pMC_mult.so dh_link -a usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.cpython-39-x86_64-linux-gnu.so usr/share/pdb2pqr/pdb2pka/substruct/Algorithms.so make[1]: Leaving directory '/build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg' dh_strip_nondeterminism -a dh_compress -a debian/rules override_dh_fixperms-arch make[1]: Entering directory '/build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg' dh_fixperms -a chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main_cgi.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/ligandclean/__init__.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pka_routines.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/src/errors.py chmod +x debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py chmod +x debian/pdb2pqr/usr/share/pdb2pqr/src/psize.py make[1]: Leaving directory '/build/pdb2pqr-aZAk4g/pdb2pqr-2.1.1+dfsg' dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_2.1.1+dfsg-7+b1_amd64.deb'. dpkg-deb: building package 'pdb2pqr-dbgsym' in '../pdb2pqr-dbgsym_2.1.1+dfsg-7+b1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../pdb2pqr_2.1.1+dfsg-7+b1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/pdb2pqr-aZAk4g /tmp/pdb2pqr-2.1.1+dfsg-7+b1qkuf21ag I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.PqipE9mc63... I: success in 662.5150 seconds md5: pdb2pqr-dbgsym_2.1.1+dfsg-7+b1_amd64.deb: OK md5: Value of 'md5' differs for pdb2pqr_2.1.1+dfsg-7+b1_amd64.deb md5: Size differs for pdb2pqr_2.1.1+dfsg-7+b1_amd64.deb sha1: pdb2pqr-dbgsym_2.1.1+dfsg-7+b1_amd64.deb: OK sha1: Value of 'sha1' differs for pdb2pqr_2.1.1+dfsg-7+b1_amd64.deb sha1: Size differs for pdb2pqr_2.1.1+dfsg-7+b1_amd64.deb sha256: pdb2pqr-dbgsym_2.1.1+dfsg-7+b1_amd64.deb: OK sha256: Value of 'sha256' differs for pdb2pqr_2.1.1+dfsg-7+b1_amd64.deb sha256: Size differs for pdb2pqr_2.1.1+dfsg-7+b1_amd64.deb Checksums: FAIL diffoscope run passed