Sat Mar 26 19:00:15 UTC 2022 I: starting to build pdb2pqr/bullseye/amd64 on jenkins on '2022-03-26 19:00' Sat Mar 26 19:00:15 UTC 2022 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_1/5782/console.log Sat Mar 26 19:00:15 UTC 2022 I: Downloading source for bullseye/pdb2pqr=2.1.1+dfsg-7+deb11u1 --2022-03-26 19:00:15-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/pdb2pqr/pdb2pqr_2.1.1%2bdfsg-7%2bdeb11u1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2342 (2.3K) Saving to: ‘pdb2pqr_2.1.1+dfsg-7+deb11u1.dsc’ 0K .. 100% 222M=0s 2022-03-26 19:00:15 (222 MB/s) - ‘pdb2pqr_2.1.1+dfsg-7+deb11u1.dsc’ saved [2342/2342] Sat Mar 26 19:00:15 UTC 2022 I: pdb2pqr_2.1.1+dfsg-7+deb11u1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pdb2pqr Binary: pdb2pqr, pdb2pqr-doc Architecture: any all Version: 2.1.1+dfsg-7+deb11u1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Manuel Prinz , Andreas Tille Homepage: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/pdb2pqr Vcs-Git: https://salsa.debian.org/med-team/pdb2pqr.git Testsuite: autopkgtest Testsuite-Triggers: python3-networkx Build-Depends: debhelper-compat (= 12), dh-python, gfortran, swig, xmlto, openbabel, python3-dev, python3-numpy, scons (>= 3.1.1-4), dos2unix, pkg-config Package-List: pdb2pqr deb science optional arch=any pdb2pqr-doc deb doc optional arch=all Checksums-Sha1: f32a6fdea111872ca6b3467f742f98dfdac91c7e 5191276 pdb2pqr_2.1.1+dfsg.orig.tar.xz 4d6d34cd7e8892c9b41e56cf80a0f095266894fd 67548 pdb2pqr_2.1.1+dfsg-7+deb11u1.debian.tar.xz Checksums-Sha256: aef49fcf96c8990275d956c02003f4b8398c665a0defb06c8655905bbf44c43b 5191276 pdb2pqr_2.1.1+dfsg.orig.tar.xz 9a12d53ed9839ac06059f64a77a9f18ba4eb3239cd5fe38ef25236f27af59641 67548 pdb2pqr_2.1.1+dfsg-7+deb11u1.debian.tar.xz Files: 6ffad71b2b018b57f44cec20d93ef161 5191276 pdb2pqr_2.1.1+dfsg.orig.tar.xz 7ca562e5590185f9da23bf383c9544b1 67548 pdb2pqr_2.1.1+dfsg-7+deb11u1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmIRO5USHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKH1T8P/1/yexjz1bh9CFOo6KCrIG2S5oczqz7G bsWdaqMnumlHmLSDOjIsexuZaPyerEgTQZNMckhVJLy5vFV2CbKULHZ9DkKwU4ze 5Epy/RQ+1+lGk6aTqYXEUQ887avIVaI0ydZv7Y/eG3JGGAXzQjMLQPGiW7pZEezM eOkp01NT2VNvPYE3MVPYCwDgo1bdLgE+jboAt7x+RUWWNK9Lir/ZPoTi5fpbr1iG 5Bm9HqFCycaztfb/6RkIS8IClSkMrHmmwodV03E6hEhpLxLqlhTuHDUEk+l+P6Ds nt8GwWFScqThGk3EAgIha1mhG2pAi0ALVqpgEliX+o6fPtAHlBbhxpOudj5LA3hx SwdePuhe9X8oBsmVfANXzoCDlot4e6YTQocMf8/OEBu3qvy6pHpC57soyTgpc7eF +U7MD395loBrcHV4TgW/jMr4ZLZqTos4uVuwxmLQiGtmCV/Sh/8/1JlMCK+aOwtj P3u3vRWKCUUgF3ZCUcfFm7VUKjeYJtnHTujo9D0rGY39QE7/FpffQTRzSSz4CUAN BOUsKut6+rrF4vI0ekBK2RGCtINUHZ7W3gjn92XAtT2H6Np/BU86/6zJ/Tc5dmHq oT7SEJuZXx3KGPEUxlhNQGAc0QBSRRvxQ8AVjuLb6K+2HELKSgAp1ffBdDk8Myx5 Gd9+oKKh0cjW =b+0A -----END PGP SIGNATURE----- Sat Mar 26 19:00:15 UTC 2022 I: Checking whether the package is not for us Sat Mar 26 19:00:15 UTC 2022 I: Starting 1st build on remote node ionos1-amd64.debian.net. Sat Mar 26 19:00:15 UTC 2022 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Sat Mar 26 19:05:54 UTC 2022 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Mar 26 07:00:24 -12 2022 I: pbuilder-time-stamp: 1648321224 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [pdb2pqr_2.1.1+dfsg-7+deb11u1.dsc] I: copying [./pdb2pqr_2.1.1+dfsg.orig.tar.xz] I: copying [./pdb2pqr_2.1.1+dfsg-7+deb11u1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.0bc1pZFt/trustedkeys.kbx': General error gpgv: Signature made Sat Feb 19 06:48:53 2022 -12 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pdb2pqr_2.1.1+dfsg-7+deb11u1.dsc dpkg-source: info: extracting pdb2pqr in 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+deb11u1.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: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/553446/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='0dafd3b96ba548babbe7e05470a9f6ee' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='553446' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.az38lfu6Bf/pbuilderrc_LzUH --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.az38lfu6Bf/b1 --logfile b1/build.log pdb2pqr_2.1.1+dfsg-7+deb11u1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 5.10.0-12-amd64 #1 SMP Debian 5.10.103-1 (2022-03-07) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 08:10 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 08:10 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 08:10 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 08:10 more -rwsr-xr-x 1 root root 55528 Jan 20 08:10 mount -rwxr-xr-x 1 root root 18664 Jan 20 08:10 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 06:12 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Mar 20 21:25 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 08:10 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 08:10 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 08:10 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/553446/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), dh-python, gfortran, swig, xmlto, openbabel, python3-dev, python3-numpy, scons (>= 3.1.1-4), dos2unix, pkg-config dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19655 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig is not installed. pbuilder-satisfydepends-dummy depends on xmlto; however: Package xmlto is not installed. pbuilder-satisfydepends-dummy depends on openbabel; however: Package openbabel is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on scons (>= 3.1.1-4); however: Package scons is not installed. pbuilder-satisfydepends-dummy depends on dos2unix; however: Package dos2unix is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docbook-xml{a} docbook-xsl{a} dos2unix{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} gfortran{a} gfortran-10{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgfortran-10-dev{a} libgfortran5{a} libglib2.0-0{a} libicu67{a} libinchi1{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} libmaeparser1{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libopenbabel7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.9{a} libpython3.9-dev{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxml2-utils{a} libxrender1{a} libxslt1.1{a} m4{a} man-db{a} media-types{a} openbabel{a} pkg-config{a} po-debconf{a} python3{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pkg-resources{a} python3.9{a} python3.9-dev{a} python3.9-minimal{a} readline-common{a} scons{a} sensible-utils{a} sgml-base{a} sgml-data{a} swig{a} swig4.0{a} ucf{a} xml-core{a} xmlto{a} xsltproc{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dblatex fop javascript-common libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl libpaper-utils lynx shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 63.0 MB of archives. After unpacking 244 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u3 [98.5 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 sgml-base all 1.30 [15.1 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u1 [693 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 python3-distutils all 3.9.2-1 [143 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 docbook-xml all 4.5-9 [84.4 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 docbook-xsl all 1.79.2+dfsg-1 [1237 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 dos2unix amd64 7.4.1-1 [392 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libgfortran-10-dev amd64 10.2.1-6 [769 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 gfortran-10 amd64 10.2.1-6 [9447 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 gfortran amd64 4:10.2.1-1 [1428 B] Get: 60 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1 [418 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.40.0-1 [543 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1 [311 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1 [772 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libexpat1-dev amd64 2.2.10-2+deb11u3 [141 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libinchi1 amd64 1.03+dfsg-3 [430 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3 [2166 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libmaeparser1 amd64 1.2.4-1+b1 [88.2 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libopenbabel7 amd64 3.1.1+dfsg-6 [3138 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libpython3.9 amd64 3.9.2-1 [1691 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-dev amd64 3.9.2-1 [4028 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libpython3-dev amd64 3.9.2-3 [21.7 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libxml2-utils amd64 2.9.10+dfsg-6.7+deb11u1 [109 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libxslt1.1 amd64 1.1.34-4 [239 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 openbabel amd64 3.1.1+dfsg-6 [134 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 python3.9-dev amd64 3.9.2-1 [515 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 python3-dev amd64 3.9.2-3 [24.8 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 python3-numpy amd64 1:1.19.5-1 [2693 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 scons all 4.0.1+dfsg-2 [559 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 swig4.0 amd64 4.0.2-1 [1377 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 swig all 4.0.2-1 [330 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 xsltproc amd64 1.1.34-4 [124 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 xmlto amd64 0.0.28-2.1 [33.6 kB] Fetched 63.0 MB in 4s (14.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../3-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:amd64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.2.10-2+deb11u3_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2+deb11u3) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_amd64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:amd64 (3.9.2-1) ... Setting up libexpat1:amd64 (2.2.10-2+deb11u3) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (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 ... 20522 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../2-libmpdec3_2.5.1-1_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../4-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:amd64. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_amd64.deb ... Unpacking libpython3.9-stdlib:amd64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_amd64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (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 ... 20943 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sgml-base. Preparing to unpack .../01-sgml-base_1.30_all.deb ... Unpacking sgml-base (1.30) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../04-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package ucf. Preparing to unpack .../07-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../08-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../09-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../10-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../11-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../12-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../13-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../14-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../15-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../16-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../17-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../18-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../21-libelf1_0.183-1_amd64.deb ... Unpacking libelf1:amd64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.13+20210201-1_amd64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../23-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.9.10+dfsg-6.7+deb11u1_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7+deb11u1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.21-4_amd64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../29-python3-lib2to3_3.9.2-1_all.deb ... Unpacking python3-lib2to3 (3.9.2-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../30-python3-distutils_3.9.2-1_all.deb ... Unpacking python3-distutils (3.9.2-1) ... Selecting previously unselected package dh-python. Preparing to unpack .../31-dh-python_4.20201102+nmu1_all.deb ... Unpacking dh-python (4.20201102+nmu1) ... Selecting previously unselected package xml-core. Preparing to unpack .../32-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package sgml-data. Preparing to unpack .../33-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook-xml. Preparing to unpack .../34-docbook-xml_4.5-9_all.deb ... Unpacking docbook-xml (4.5-9) ... Selecting previously unselected package docbook-xsl. Preparing to unpack .../35-docbook-xsl_1.79.2+dfsg-1_all.deb ... Unpacking docbook-xsl (1.79.2+dfsg-1) ... Selecting previously unselected package dos2unix. Preparing to unpack .../36-dos2unix_7.4.1-1_amd64.deb ... Unpacking dos2unix (7.4.1-1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../37-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../38-fontconfig-config_2.13.1-4.2_all.deb ... Unpacking fontconfig-config (2.13.1-4.2) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../39-libgfortran5_10.2.1-6_amd64.deb ... Unpacking libgfortran5:amd64 (10.2.1-6) ... Selecting previously unselected package libgfortran-10-dev:amd64. Preparing to unpack .../40-libgfortran-10-dev_10.2.1-6_amd64.deb ... Unpacking libgfortran-10-dev:amd64 (10.2.1-6) ... Selecting previously unselected package gfortran-10. Preparing to unpack .../41-gfortran-10_10.2.1-6_amd64.deb ... Unpacking gfortran-10 (10.2.1-6) ... Selecting previously unselected package gfortran. Preparing to unpack .../42-gfortran_4%3a10.2.1-1_amd64.deb ... Unpacking gfortran (4:10.2.1-1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../43-libblas3_3.9.0-3_amd64.deb ... Unpacking libblas3:amd64 (3.9.0-3) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../44-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libmd0:amd64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/pdb2pqr-2.1.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pdb2pqr_2.1.1+dfsg-7+deb11u1_source.changes dpkg-buildpackage: info: source package pdb2pqr dpkg-buildpackage: info: source version 2.1.1+dfsg-7+deb11u1 dpkg-buildpackage: info: source distribution bullseye dpkg-buildpackage: info: source changed by Andrius Merkys 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-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-2.1.1+dfsg' dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/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-2.1.1+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_install-arch make[1]: Entering directory '/build/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-2.1.1+dfsg' dh_install -Npdb2pqr dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/pdb2pqr-2.1.1+dfsg' dh_installchangelogs ChangeLog.md make[1]: Leaving directory '/build/pdb2pqr-2.1.1+dfsg' debian/rules override_dh_installexamples make[1]: Entering directory '/build/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-2.1.1+dfsg' debian/rules override_dh_installman-arch make[1]: Entering directory '/build/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-2.1.1+dfsg' dh_python3 dh_perl debian/rules override_dh_link-arch make[1]: Entering directory '/build/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-2.1.1+dfsg' dh_link -Npdb2pqr dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms-arch make[1]: Entering directory '/build/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-2.1.1+dfsg' dh_fixperms -Npdb2pqr dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'pdb2pqr-dbgsym' in '../pdb2pqr-dbgsym_2.1.1+dfsg-7+deb11u1_amd64.deb'. dpkg-deb: building package 'pdb2pqr-doc' in '../pdb2pqr-doc_2.1.1+dfsg-7+deb11u1_all.deb'. dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/553446 and its subdirectories I: Current time: Sat Mar 26 07:05:53 -12 2022 I: pbuilder-time-stamp: 1648321553 Sat Mar 26 19:05:54 UTC 2022 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Sat Mar 26 19:05:54 UTC 2022 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Sat Mar 26 19:09:22 UTC 2022 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Sat Mar 26 19:09:22 UTC 2022 I: pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.changes: Format: 1.8 Date: Wed, 16 Feb 2022 02:13:35 -0500 Source: pdb2pqr Binary: pdb2pqr pdb2pqr-dbgsym pdb2pqr-doc Architecture: amd64 all Version: 2.1.1+dfsg-7+deb11u1 Distribution: bullseye Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andrius Merkys Description: pdb2pqr - Preparation of protein structures for electrostatics calculations pdb2pqr-doc - example files accompanying pdb2pqr Changes: pdb2pqr (2.1.1+dfsg-7+deb11u1) bullseye; urgency=medium . * Team upload. * Fix ImportError in propka due to changed relative import handling in Python 3.8. The patch fixing #937262 has changed the way relative imports are called, but the used construction does not work since Python 3.8. Undoing changes in the patch fixed the ImportError in propka. Checksums-Sha1: f8fd4e94a04299f1d0ea4b734e53a7a17a2f81ef 285684 pdb2pqr-dbgsym_2.1.1+dfsg-7+deb11u1_amd64.deb 186b1c399f7b92d1f7d607d7f17b2346d6eb2050 471868 pdb2pqr-doc_2.1.1+dfsg-7+deb11u1_all.deb 2ee0bb4ade1719378810df1d612ca6eea744df67 7656 pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.buildinfo 0e62ee84e96fda9d6d680c952e555a78390ed09a 391180 pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.deb Checksums-Sha256: e9fe03dc134b82c1b28373a9b3eb374e38b7eb8c1ff158c7cb2acdebf2e09b1e 285684 pdb2pqr-dbgsym_2.1.1+dfsg-7+deb11u1_amd64.deb 4fb8e685f3344be2cf9ffb2d15da3cd763ec156c110267fdb9806991ce6d1c8c 471868 pdb2pqr-doc_2.1.1+dfsg-7+deb11u1_all.deb 6b909b9d23a3aece998cb4e92a7760c994661ef205ce880ac21121b0d9aa1e85 7656 pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.buildinfo c96d8e570fcb49f706e0bb76a85f7f95578f124d5f236f18f2626af688871965 391180 pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.deb Files: e2baf46ee4dfc3ed7a870616a468b871 285684 debug optional pdb2pqr-dbgsym_2.1.1+dfsg-7+deb11u1_amd64.deb 0c8ad6c4266cf849b64b3b5b48d50b04 471868 doc optional pdb2pqr-doc_2.1.1+dfsg-7+deb11u1_all.deb e8b7223e018a044123216a2d7ff9692e 7656 science optional pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.buildinfo df5a0fc51d30b4dc6a7d9b8c2626555c 391180 science optional pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.deb Sat Mar 26 19:09:23 UTC 2022 I: diffoscope 206 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/tmp.az38lfu6Bf/pdb2pqr_2.1.1+dfsg-7+deb11u1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.az38lfu6Bf/pdb2pqr_2.1.1+dfsg-7+deb11u1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.az38lfu6Bf/pdb2pqr_2.1.1+dfsg-7+deb11u1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.az38lfu6Bf/b1/pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.az38lfu6Bf/b2/pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.231s) 0.231s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.026s) 0.026s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Sat Mar 26 19:09:24 UTC 2022 I: diffoscope 206 found no differences in the changes files, and a .buildinfo file also exists. Sat Mar 26 19:09:24 UTC 2022 I: pdb2pqr from bullseye built successfully and reproducibly on amd64. Sat Mar 26 19:09:25 UTC 2022 I: Submitting .buildinfo files to external archives: Sat Mar 26 19:09:25 UTC 2022 I: Submitting 12K b1/pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.buildinfo.asc Sat Mar 26 19:09:27 UTC 2022 I: Submitting 12K b2/pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.buildinfo.asc Sat Mar 26 19:09:28 UTC 2022 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Mar 26 19:09:28 UTC 2022 I: Done submitting .buildinfo files. Sat Mar 26 19:09:28 UTC 2022 I: Removing signed pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.buildinfo.asc files: removed './b1/pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.buildinfo.asc' removed './b2/pdb2pqr_2.1.1+dfsg-7+deb11u1_amd64.buildinfo.asc'