Mon Apr 5 16:27:16 UTC 2021 I: starting to build pdb2pqr/buster/amd64 on jenkins on '2021-04-05 16:27' Mon Apr 5 16:27:16 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_21/1601/console.log Mon Apr 5 16:27:16 UTC 2021 I: Downloading source for buster/pdb2pqr=2.1.1+dfsg-5 --2021-04-05 16:27:17-- http://deb.debian.org/debian/pool/main/p/pdb2pqr/pdb2pqr_2.1.1+dfsg-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2277 (2.2K) Saving to: ‘pdb2pqr_2.1.1+dfsg-5.dsc’ 0K .. 100% 180M=0s 2021-04-05 16:27:17 (180 MB/s) - ‘pdb2pqr_2.1.1+dfsg-5.dsc’ saved [2277/2277] Mon Apr 5 16:27:17 UTC 2021 I: pdb2pqr_2.1.1+dfsg-5.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-5 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: 4.1.5 Vcs-Browser: https://salsa.debian.org/med-team/pdb2pqr Vcs-Git: https://salsa.debian.org/med-team/pdb2pqr.git Testsuite: autopkgtest Testsuite-Triggers: python-networkx Build-Depends: debhelper (>= 11~), dh-python, gfortran, swig, xmlto, openbabel, python-dev, python-numpy, scons, dos2unix 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 a4ae85ad0c0a45cb1d60b03c74aac998908b7441 13480 pdb2pqr_2.1.1+dfsg-5.debian.tar.xz Checksums-Sha256: aef49fcf96c8990275d956c02003f4b8398c665a0defb06c8655905bbf44c43b 5191276 pdb2pqr_2.1.1+dfsg.orig.tar.xz adfbca35964183db2ff81b4dbe075a6765a52584a0870e7824fe7aea85926299 13480 pdb2pqr_2.1.1+dfsg-5.debian.tar.xz Files: 6ffad71b2b018b57f44cec20d93ef161 5191276 pdb2pqr_2.1.1+dfsg.orig.tar.xz 5a3b2543d1a91c5e616b032da29ea658 13480 pdb2pqr_2.1.1+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAlzrhxcSHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHcOMP/1FtVcYtxXltoWHf5oWhpkoPzLVULXds 2fMGcIjDlutvKYuDgmyFprYuSOeNgiHKjssofM6HnJy3Ci57isYECYH1nDgxwDYF ja719m75bN/BgSB+vVpSiDIju2kC6/yJjBkbZVBtia3N6PZU47c7V+Y4P3r0R9+7 xC+KZHtvUmTFNlHjt8vmqT99DH6D8qJfYvADDS0tOH582JlUGhdCMW4TRM0JAURG NHDu3lzCzNB1gL004N+Te4z2p+mj28Swz31pb3w98o0daEX4BzmeIVtRBpfiLIz9 Y2kFZ3ZkZtjLpRxt+1NXF6GOg0IzMZg/1n4qhDUwkdoOg8ZG0PNwBSj4tbIQFmYX s1afL9BRfOOYW+cmdQ5ewLSDUnIGpI52WOaqUATdYePSIknyksThG8wAtnFtvrlH HezWXgC46SSU8+3FluIITNOjt8hJxycA8Vzo7XvKizoAD+yQSp+IH1iAAr/xqhZJ DT0t4S6v5bs7eSoPG6MH07XjNrtXWJCEedaLfPZPJIMIheDvoLzpyPnlDoDil3h7 LZ98sxxn/S9R/9DRXsZZkDWtImVewVLft7XBxPsbysfadzLy03ewiz3l7lmxuRNG 5LDMd0t7MT8N7mfymU1HzBq/yqFGpjupLydlc7eKqMvJQliNSHgTBijXqP4HNYMt lFPzOVVO66qP =Bxuw -----END PGP SIGNATURE----- Mon Apr 5 16:27:17 UTC 2021 I: Checking whether the package is not for us Mon Apr 5 16:27:17 UTC 2021 I: Starting 1st build on remote node ionos11-amd64.debian.net. Mon Apr 5 16:27:17 UTC 2021 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Mon Apr 5 16:28:29 UTC 2021 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Apr 5 04:27:19 -12 2021 I: pbuilder-time-stamp: 1617640039 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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-5.dsc] I: copying [./pdb2pqr_2.1.1+dfsg.orig.tar.xz] I: copying [./pdb2pqr_2.1.1+dfsg-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun May 26 18:43:35 2019 -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-5.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-5.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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/32465/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 parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='21be769aa421401dbad2868678eb90cd' 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='32465' 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.WqSMdEIaRv/pbuilderrc_373q --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.WqSMdEIaRv/b1 --logfile b1/build.log pdb2pqr_2.1.1+dfsg-5.dsc' SUDO_GID='111' SUDO_UID='106' 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 ionos11-amd64 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Mar 20 20:25 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/32465/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 (>= 11~), dh-python, gfortran, swig, xmlto, openbabel, python-dev, python-numpy, scons, dos2unix dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 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 (>= 11~); however: Package debhelper 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 python-dev; however: Package python-dev is not installed. pbuilder-satisfydepends-dummy depends on python-numpy; however: Package python-numpy is not installed. pbuilder-satisfydepends-dummy depends on scons; however: Package scons is not installed. pbuilder-satisfydepends-dummy depends on dos2unix; however: Package dos2unix 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} bsdmainutils{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-8{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbsd0{a} libcairo2{a} libcroco3{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgfortran-8-dev{a} libgfortran5{a} libglib2.0-0{a} libicu63{a} liblapack3{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libopenbabel5{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpython-dev{a} libpython-stdlib{a} libpython2-dev{a} libpython2-stdlib{a} libpython2.7{a} libpython2.7-dev{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{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} mime-support{a} openbabel{a} po-debconf{a} python{a} python-dev{a} python-minimal{a} python-numpy{a} python-pkg-resources{a} python2{a} python2-dev{a} python2-minimal{a} python2.7{a} python2.7-dev{a} python2.7-minimal{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.7{a} python3.7-minimal{a} readline-common{a} scons{a} sensible-utils{a} sgml-base{a} sgml-data{a} swig{a} swig3.0{a} ucf{a} xml-core{a} xmlto{a} xsltproc{a} The following packages are RECOMMENDED but will NOT be installed: curl dblatex fop libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libpaper-utils lynx shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 107 newly installed, 0 to remove and 0 not upgraded. Need to get 91.2 MB of archives. After unpacking 288 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u5 [1539 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 sgml-base all 1.29 [14.8 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u2 [1258 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u1 [689 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 dh-python all 3.20190308 [99.3 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 sgml-data all 2.0.11 [179 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 docbook-xml all 4.5-8 [84.7 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 docbook-xsl all 1.79.1+dfsg-2 [1249 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 dos2unix amd64 7.4.0-1 [391 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libgfortran-8-dev amd64 8.3.0-6 [616 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 gfortran-8 amd64 8.3.0-6 [9375 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 gfortran amd64 4:8.3.0-1 [1432 B] Get: 73 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u1 [294 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u1 [757 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 libcairo2 amd64 1.16.0-4+deb10u1 [688 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libexpat1-dev amd64 2.2.6-2+deb10u1 [153 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libopenbabel5 amd64 2.4.1+dfsg-3 [3003 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libpython2.7 amd64 2.7.16-2+deb10u1 [1036 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libpython2.7-dev amd64 2.7.16-2+deb10u1 [31.6 MB] Get: 93 http://deb.debian.org/debian buster/main amd64 libpython2-dev amd64 2.7.16-1 [20.9 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 libpython-dev amd64 2.7.16-1 [20.9 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 libxml2-utils amd64 2.9.4+dfsg1-7+deb10u1 [99.6 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 libxslt1.1 amd64 1.1.32-2.2~deb10u1 [237 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 openbabel amd64 2.4.1+dfsg-3 [128 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 python2.7-dev amd64 2.7.16-2+deb10u1 [294 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 python2-dev amd64 2.7.16-1 [1212 B] Get: 100 http://deb.debian.org/debian buster/main amd64 python-dev amd64 2.7.16-1 [1192 B] Get: 101 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 python-numpy amd64 1:1.16.2-1 [2101 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 scons all 3.0.1-2 [538 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 swig3.0 amd64 3.0.12-2 [1397 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 swig amd64 3.0.12-2 [310 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 xsltproc amd64 1.1.32-2.2~deb10u1 [122 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 xmlto amd64 0.0.28-2.1 [33.6 kB] Fetched 91.2 MB in 2s (57.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_amd64.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_amd64.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u5_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u5) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../14-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_amd64.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:amd64. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_amd64.deb ... Unpacking libpython2-stdlib:amd64 (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:amd64. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.16-1) ... Setting up libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 20658 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_amd64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (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 ... 20691 files and directories currently installed.) Preparing to unpack .../python_2.7.16-1_amd64.deb ... Unpacking python (2.7.16-1) ... Selecting previously unselected package libpython3.7-minimal:amd64. Preparing to unpack .../libpython3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../python3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u3) ... Setting up libssl1.1:amd64 (1.1.1d-0+deb10u5) ... Setting up libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u3) ... 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 ... 20945 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.7.3-1_amd64.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package libmpdec2:amd64. Preparing to unpack .../libmpdec2_2.4.2-2_amd64.deb ... Unpacking libmpdec2:amd64 (2.4.2-2) ... Selecting previously unselected package libpython3.7-stdlib:amd64. Preparing to unpack .../libpython3.7-stdlib_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package python3.7. Preparing to unpack .../python3.7_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7 (3.7.3-2+deb10u3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../libpython3-stdlib_3.7.3-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... 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 ... 21357 files and directories currently installed.) Preparing to unpack .../00-python3_3.7.3-1_amd64.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../01-sgml-base_1.29_all.deb ... Unpacking sgml-base (1.29) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../04-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package ucf. Preparing to unpack .../07-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../08-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../09-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../10-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../11-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../12-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../13-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../14-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../15-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../16-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../17-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../18-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../19-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../20-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../21-libglib2.0-0_2.58.3-2+deb10u2_amd64.deb ... 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Setting up xmlto (0.0.28-2.1) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 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 dpkg-buildpackage: info: source package pdb2pqr dpkg-buildpackage: info: source version 2.1.1+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python2 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 build dh build --with python2 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 ) python scons/scons.py \ 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/python2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include pdb2pka/substruct/Algorithms.cpp In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1822, from /usr/include/python2.7/numpy/ndarrayobject.h:12, from /usr/include/python2.7/numpy/arrayobject.h:4, from pdb2pka/substruct/Algorithms.cpp:43: /usr/include/python2.7/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] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ g++ -o pdb2pka/substruct/Algorithms.so -Wl,-z,relro -Wl,-z,now -shared pdb2pka/substruct/Algorithms.os -L/usr/lib -lpython2.7 g++ -o pdb2pka/pMC_mult.os -c -g -fPIC -I/usr/include/python2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include pdb2pka/pMC_mult.cpp g++ -o pdb2pka/pMC_mult_wrap.os -c -g -fPIC -I/usr/include/python2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include pdb2pka/pMC_mult_wrap.cpp g++ -o pdb2pka/_pMC_mult.so -Wl,-z,relro -Wl,-z,now -shared pdb2pka/pMC_mult.os pdb2pka/pMC_mult_wrap.os -L/usr/lib -lpython2.7 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.so', 'pdb2pka/_pMC_mult.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 python that you intend to use with pdb2pqr. For example: "/opt/bin/python scons/scons.py" will setup pdb2pqr to be run with /opt/bin/python Run "python scons/scons.py install" to install pdb2pqr in /usr/share/pdb2pqr/ Run "python scons/scons.py basic-test" for a basic functionality test Run "python scons/scons.py advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled. Run "python scons/scons.py complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled. Run "python scons/scons.py pdb2pka-test" for a test of PDB2PKA functionality. Requires numpy, PDB2PKA support compiled AND the APBS python 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/scons.py install" Run "python scons/scons.py 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 fakeroot debian/rules binary dh binary --with python2 dh_testroot 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' dh_installexamples 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_python2 I: dh_python2 tools:114: replacing shebang in debian/pdb2pqr/usr/share/pdb2pqr/pdb2pqr.py dh_perl dh_link 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_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'pdb2pqr-doc' in '../pdb2pqr-doc_2.1.1+dfsg-5_all.deb'. dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_2.1.1+dfsg-5_amd64.deb'. dpkg-deb: building package 'pdb2pqr-dbgsym' in '../pdb2pqr-dbgsym_2.1.1+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pdb2pqr_2.1.1+dfsg-5_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) 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/32465 and its subdirectories I: Current time: Mon Apr 5 04:28:29 -12 2021 I: pbuilder-time-stamp: 1617640109 Mon Apr 5 16:28:30 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Mon Apr 5 16:28:30 UTC 2021 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Mon Apr 5 16:30:19 UTC 2021 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Mon Apr 5 16:30:19 UTC 2021 I: pdb2pqr_2.1.1+dfsg-5_amd64.changes: Format: 1.8 Date: Mon, 27 May 2019 01:52:46 -0400 Source: pdb2pqr Binary: pdb2pqr pdb2pqr-dbgsym pdb2pqr-doc Architecture: amd64 all Version: 2.1.1+dfsg-5 Distribution: unstable 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 Closes: 903759 Changes: pdb2pqr (2.1.1+dfsg-5) unstable; urgency=medium . * Team upload. . [ Andreas Tille ] * Build-Depends: dh-python . [ Andrius Merkys ] * Fixing autopkgtest 'installation-test' by substituting non-existent PDB file with an existing one. Removing autopkgtest 'ligands-test' as it depended on files that are not shipped by the upstream anymore. (Closes: #903759) Checksums-Sha1: 4823b6e693cf436d9f1b021f9bea4380d3726a4f 313384 pdb2pqr-dbgsym_2.1.1+dfsg-5_amd64.deb 82858841b8f335c56eadfd79d70c26105ca90a81 475716 pdb2pqr-doc_2.1.1+dfsg-5_all.deb be97ae0589acff6a5f52db6032aca8707bd4bbfa 7211 pdb2pqr_2.1.1+dfsg-5_amd64.buildinfo 8d1347a4c62d70d70cdfde6651325aa5c83eee1c 384832 pdb2pqr_2.1.1+dfsg-5_amd64.deb Checksums-Sha256: d42f8967982a9773b3a7c8560980fd6d151161ae976e872dc19521b257def52e 313384 pdb2pqr-dbgsym_2.1.1+dfsg-5_amd64.deb 88abc3091fc4bfc42d1cf07faeaa4e42c771f8ca8402ac29d175673f7f604907 475716 pdb2pqr-doc_2.1.1+dfsg-5_all.deb 07e6f91c63758b1773f3f138508081df106c10a268b6ab04b2fed319a72f4890 7211 pdb2pqr_2.1.1+dfsg-5_amd64.buildinfo 9f3b29d600ee1b6a4bfc052cdf296ed3c9198bab41bdaa6a87b5cc2da65cc723 384832 pdb2pqr_2.1.1+dfsg-5_amd64.deb Files: 8ffd637c270303bc499e0efa31214854 313384 debug optional pdb2pqr-dbgsym_2.1.1+dfsg-5_amd64.deb 45e9d444a0c3a93b12cad5f93347529c 475716 doc optional pdb2pqr-doc_2.1.1+dfsg-5_all.deb 1e3b5936e1b2ed114168d8aaa40390cc 7211 science optional pdb2pqr_2.1.1+dfsg-5_amd64.buildinfo 57edcddbaa27cb8c77a9184a4e084b51 384832 science optional pdb2pqr_2.1.1+dfsg-5_amd64.deb Mon Apr 5 16:30:21 UTC 2021 I: diffoscope 170 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.WqSMdEIaRv/pdb2pqr_2.1.1+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.WqSMdEIaRv/pdb2pqr_2.1.1+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.WqSMdEIaRv/pdb2pqr_2.1.1+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.WqSMdEIaRv/b1/pdb2pqr_2.1.1+dfsg-5_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.WqSMdEIaRv/b2/pdb2pqr_2.1.1+dfsg-5_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: 0.362s) 0.362s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.055s) 0.054s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Apr 5 16:30:23 UTC 2021 I: diffoscope 170 found no differences in the changes files, and a .buildinfo file also exists. Mon Apr 5 16:30:23 UTC 2021 I: pdb2pqr from buster built successfully and reproducibly on amd64. Mon Apr 5 16:30:25 UTC 2021 I: Submitting .buildinfo files to external archives: Mon Apr 5 16:30:25 UTC 2021 I: Submitting 8.0K b1/pdb2pqr_2.1.1+dfsg-5_amd64.buildinfo.asc Mon Apr 5 16:30:26 UTC 2021 I: Submitting 8.0K b2/pdb2pqr_2.1.1+dfsg-5_amd64.buildinfo.asc Mon Apr 5 16:30:28 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Apr 5 16:30:28 UTC 2021 I: Done submitting .buildinfo files. Mon Apr 5 16:30:28 UTC 2021 I: Removing signed pdb2pqr_2.1.1+dfsg-5_amd64.buildinfo.asc files: removed './b1/pdb2pqr_2.1.1+dfsg-5_amd64.buildinfo.asc' removed './b2/pdb2pqr_2.1.1+dfsg-5_amd64.buildinfo.asc'