Mon Mar 28 01:44:47 UTC 2022 I: starting to build pdb2pqr/bullseye/i386 on jenkins on '2022-03-28 01:44' Mon Mar 28 01:44:47 UTC 2022 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_7/4014/console.log Mon Mar 28 01:44:47 UTC 2022 I: Downloading source for bullseye/pdb2pqr=2.1.1+dfsg-7+deb11u1 --2022-03-28 01:44:47-- 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% 326M=0s 2022-03-28 01:44:47 (326 MB/s) - ‘pdb2pqr_2.1.1+dfsg-7+deb11u1.dsc’ saved [2342/2342] Mon Mar 28 01:44:47 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----- Mon Mar 28 01:44:47 UTC 2022 I: Checking whether the package is not for us Mon Mar 28 01:44:47 UTC 2022 I: Starting 1st build on remote node ionos12-i386.debian.net. Mon Mar 28 01:44:47 UTC 2022 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Mon Mar 28 01:46:08 UTC 2022 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Mar 27 13:44:48 -12 2022 I: pbuilder-time-stamp: 1648431888 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: using eatmydata during job 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.HiNGGrLu/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/1997/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='e77a7ce4c7e14f26abf8a6525ff32f36' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='1997' 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.GzvVW2do5d/pbuilderrc_RWeM --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.GzvVW2do5d/b1 --logfile b1/build.log pdb2pqr_2.1.1+dfsg-7+deb11u1.dsc' SUDO_GID='112' SUDO_UID='107' 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 ionos12-i386 5.10.0-12-686-pae #1 SMP Debian 5.10.103-1 (2022-03-07) i686 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Aug 4 2021 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 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 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 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 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 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 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 71928 Jan 20 08:10 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 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 100952 Mar 2 2021 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Jan 20 08:10 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Jan 20 08:10 more -rwsr-xr-x 1 root root 50720 Jan 20 08:10 mount -rwxr-xr-x 1 root root 13856 Jan 20 08:10 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 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 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Mar 21 22:43 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Jan 20 08:10 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Jan 20 08:10 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 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/1997/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: i386 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 ... 19675 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 64.3 MB of archives. After unpacking 249 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-8+deb11u1 [149 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2+deb11u3 [101 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 sgml-base all 1.30 [15.1 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 ucf all 3.0043 [74.0 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7+deb11u1 [728 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 python3-distutils all 3.9.2-1 [143 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 xml-core all 0.18+nmu1 [23.8 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 sgml-data all 2.0.11+nmu1 [179 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 docbook-xml all 4.5-9 [84.4 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 docbook-xsl all 1.79.2+dfsg-1 [1237 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 dos2unix i386 7.4.1-1 [394 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 libgfortran-10-dev i386 10.2.1-6 [705 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 gfortran-10 i386 10.2.1-6 [9642 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 gfortran i386 4:10.2.1-1 [1436 B] Get: 60 http://deb.debian.org/debian bullseye/main i386 libblas3 i386 3.9.0-3 [147 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1 [111 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libpng16-16 i386 1.6.37-3 [303 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libfreetype6 i386 2.10.4+dfsg-1 [429 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libfontconfig1 i386 2.13.1-4.2 [358 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libpixman-1-0 i386 0.40.0-1 [545 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libxcb1 i386 1.14-3 [144 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 libx11-data all 2:1.7.2-1 [311 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 libx11-6 i386 2:1.7.2-1 [794 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 libxcb-render0 i386 1.14-3 [112 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 libxcb-shm0 i386 1.14-3 [102 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 libxext6 i386 2:1.3.3-1.1 [55.2 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 libxrender1 i386 1:0.9.10-1 [34.1 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 libcairo2 i386 1.16.0-5 [746 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 libexpat1-dev i386 2.2.10-2+deb11u3 [149 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 libglib2.0-0 i386 2.66.8-1 [1437 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 libinchi1 i386 1.03+dfsg-3 [424 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 liblapack3 i386 3.9.0-3 [1960 kB] Get: 85 http://deb.debian.org/debian bullseye/main i386 libmaeparser1 i386 1.2.4-1+b1 [94.6 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 libopenbabel7 i386 3.1.1+dfsg-6 [3277 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 libpython3.9 i386 3.9.2-1 [1715 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 libpython3.9-dev i386 3.9.2-1 [3822 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 libpython3-dev i386 3.9.2-3 [21.7 kB] Get: 90 http://deb.debian.org/debian bullseye/main i386 libxml2-utils i386 2.9.10+dfsg-6.7+deb11u1 [110 kB] Get: 91 http://deb.debian.org/debian bullseye/main i386 libxslt1.1 i386 1.1.34-4 [251 kB] Get: 92 http://deb.debian.org/debian bullseye/main i386 openbabel i386 3.1.1+dfsg-6 [136 kB] Get: 93 http://deb.debian.org/debian bullseye/main i386 pkg-config i386 0.29.2-1 [66.3 kB] Get: 94 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get: 95 http://deb.debian.org/debian bullseye/main i386 python3.9-dev i386 3.9.2-1 [515 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 python3-dev i386 3.9.2-3 [24.8 kB] Get: 97 http://deb.debian.org/debian bullseye/main i386 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 98 http://deb.debian.org/debian bullseye/main i386 python3-numpy i386 1:1.19.5-1 [3600 kB] Get: 99 http://deb.debian.org/debian bullseye/main i386 scons all 4.0.1+dfsg-2 [559 kB] Get: 100 http://deb.debian.org/debian bullseye/main i386 swig4.0 i386 4.0.2-1 [1443 kB] Get: 101 http://deb.debian.org/debian bullseye/main i386 swig all 4.0.2-1 [330 kB] Get: 102 http://deb.debian.org/debian bullseye/main i386 xsltproc i386 1.1.34-4 [124 kB] Get: 103 http://deb.debian.org/debian bullseye/main i386 xmlto i386 0.0.28-2.1 [33.9 kB] Fetched 64.3 MB in 2s (37.2 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 ... 19675 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_i386.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../1-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. 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Setting up libexpat1:i386 (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 ... 20542 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_i386.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:i386. Preparing to unpack .../2-libmpdec3_2.5.1-1_i386.deb ... Unpacking libmpdec3:i386 (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:i386. Preparing to unpack .../4-libreadline8_8.1-1_i386.deb ... Unpacking libreadline8:i386 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:i386. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_i386.deb ... Unpacking libpython3.9-stdlib:i386 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_i386.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_i386.deb ... Unpacking libpython3-stdlib:i386 (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 ... 20963 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_i386.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_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../04-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-4_i386.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:i386. Preparing to unpack .../08-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../09-m4_1.4.18-5_i386.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:i386. Preparing to unpack .../21-libelf1_0.183-1_i386.deb ... Unpacking libelf1:i386 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.13+20210201-1_i386.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:i386. Preparing to unpack .../23-libicu67_67.1-7_i386.deb ... Unpacking libicu67:i386 (67.1-7) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../24-libxml2_2.9.10+dfsg-6.7+deb11u1_i386.deb ... Unpacking libxml2:i386 (2.9.10+dfsg-6.7+deb11u1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.21-4_i386.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_i386.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:i386. Preparing to unpack .../39-libgfortran5_10.2.1-6_i386.deb ... Unpacking libgfortran5:i386 (10.2.1-6) ... Selecting previously unselected package libgfortran-10-dev:i386. Preparing to unpack .../40-libgfortran-10-dev_10.2.1-6_i386.deb ... Unpacking libgfortran-10-dev:i386 (10.2.1-6) ... Selecting previously unselected package gfortran-10. Preparing to unpack .../41-gfortran-10_10.2.1-6_i386.deb ... Unpacking gfortran-10 (10.2.1-6) ... Selecting previously unselected package gfortran. Preparing to unpack .../42-gfortran_4%3a10.2.1-1_i386.deb ... Unpacking gfortran (4:10.2.1-1) ... Selecting previously unselected package libblas3:i386. Preparing to unpack .../43-libblas3_3.9.0-3_i386.deb ... Unpacking libblas3:i386 (3.9.0-3) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../44-libbrotli1_1.0.9-2+b2_i386.deb ... Unpacking libbrotli1:i386 (1.0.9-2+b2) ... Selecting previously unselected package libmd0:i386. Preparing to unpack .../45-libmd0_1.0.3-3_i386.deb ... Unpacking libmd0:i386 (1.0.3-3) ... Selecting previously unselected package libbsd0:i386. 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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 i386 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/i386-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-i386-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/i386-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/i386-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-i386-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-i386-linux-gnu.so', 'pdb2pka/_pMC_mult.cpython-39-i386-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-i386-linux-gnu.so usr/share/pdb2pqr/pdb2pka/_pMC_mult.so dh_link -a usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.cpython-39-i386-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' in '../pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.deb'. dpkg-deb: building package 'pdb2pqr-doc' in '../pdb2pqr-doc_2.1.1+dfsg-7+deb11u1_all.deb'. dpkg-deb: building package 'pdb2pqr-dbgsym' in '../pdb2pqr-dbgsym_2.1.1+dfsg-7+deb11u1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.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/1997 and its subdirectories I: Current time: Sun Mar 27 13:46:08 -12 2022 I: pbuilder-time-stamp: 1648431968 Mon Mar 28 01:46:08 UTC 2022 I: 1st build successful. Starting 2nd build on remote node ionos16-i386.debian.net. Mon Mar 28 01:46:08 UTC 2022 I: Preparing to do remote build '2' on ionos16-i386.debian.net. Mon Mar 28 01:46:56 UTC 2022 I: Deleting $TMPDIR on ionos16-i386.debian.net. Mon Mar 28 01:46:56 UTC 2022 I: pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.changes: Format: 1.8 Date: Wed, 16 Feb 2022 02:13:35 -0500 Source: pdb2pqr Binary: pdb2pqr pdb2pqr-dbgsym pdb2pqr-doc Architecture: i386 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: ea31f2e6a58402dbaf34792d0503efd819ce68b8 281380 pdb2pqr-dbgsym_2.1.1+dfsg-7+deb11u1_i386.deb 186b1c399f7b92d1f7d607d7f17b2346d6eb2050 471868 pdb2pqr-doc_2.1.1+dfsg-7+deb11u1_all.deb 47d74e96f3ef6d4ec3cdca3ba371fce1556fed2e 7637 pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.buildinfo 3d9cd204a9b4dd286d903f3aea2387f3c718196a 399192 pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.deb Checksums-Sha256: e4d5db52ed602ebf8a7234dd0d95479d4f63d329e7437c16d6b513c895143106 281380 pdb2pqr-dbgsym_2.1.1+dfsg-7+deb11u1_i386.deb 4fb8e685f3344be2cf9ffb2d15da3cd763ec156c110267fdb9806991ce6d1c8c 471868 pdb2pqr-doc_2.1.1+dfsg-7+deb11u1_all.deb 7563b00c11bf678580c18d7fd81066eb91b4866e9eea9586a915da058f0208ce 7637 pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.buildinfo f70324abcfa8208688f381c93d5443b62071cd77da6fdeec2d65f4172fe6f1fa 399192 pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.deb Files: eacc49d450b7d8fe6238eb25c5a16afa 281380 debug optional pdb2pqr-dbgsym_2.1.1+dfsg-7+deb11u1_i386.deb 0c8ad6c4266cf849b64b3b5b48d50b04 471868 doc optional pdb2pqr-doc_2.1.1+dfsg-7+deb11u1_all.deb 9592d31f292a77c9f69f5ab481bfe73f 7637 science optional pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.buildinfo f1709040ed715f1609b592c298f93b7d 399192 science optional pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.deb Mon Mar 28 01:46:57 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.GzvVW2do5d/pdb2pqr_2.1.1+dfsg-7+deb11u1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.GzvVW2do5d/pdb2pqr_2.1.1+dfsg-7+deb11u1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.GzvVW2do5d/pdb2pqr_2.1.1+dfsg-7+deb11u1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.GzvVW2do5d/b1/pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.changes /srv/reproducible-results/rbuild-debian/tmp.GzvVW2do5d/b2/pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.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: 0.236s) 0.236s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.028s) 0.028s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Mon Mar 28 01:46:58 UTC 2022 I: diffoscope 206 found no differences in the changes files, and a .buildinfo file also exists. Mon Mar 28 01:46:58 UTC 2022 I: pdb2pqr from bullseye built successfully and reproducibly on i386. Mon Mar 28 01:46:59 UTC 2022 I: Submitting .buildinfo files to external archives: Mon Mar 28 01:46:59 UTC 2022 I: Submitting 12K b1/pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.buildinfo.asc Mon Mar 28 01:47:01 UTC 2022 I: Submitting 12K b2/pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.buildinfo.asc Mon Mar 28 01:47:01 UTC 2022 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Mar 28 01:47:01 UTC 2022 I: Done submitting .buildinfo files. Mon Mar 28 01:47:01 UTC 2022 I: Removing signed pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.buildinfo.asc files: removed './b1/pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.buildinfo.asc' removed './b2/pdb2pqr_2.1.1+dfsg-7+deb11u1_i386.buildinfo.asc'