I: pbuilder: network access will be disabled during build I: Current time: Sun Oct 25 02:56:53 +14 2020 I: pbuilder-time-stamp: 1603544213 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: using eatmydata during job 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 Mon May 27 20:43:35 2019 +14 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/6573/tmp/hooks/D01_modify_environment starting debug: Running on profitbricks-build12-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/6573/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/6573/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=81f5d0aa57c342e2b4b86d236fa56b63 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=6573 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.3pdrytqaSh/pbuilderrc_J7B5 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.3pdrytqaSh/b2 --logfile b2/build.log pdb2pqr_2.1.1+dfsg-5.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 4.19.0-12-686-pae #1 SMP Debian 4.19.152-1 (2020-10-18) i686 GNU/Linux I: ls -l /bin total 5512 -rwxr-xr-x 1 root root 1302248 Apr 18 2019 bash -rwxr-xr-x 3 root root 38280 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 17768 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 38692 Mar 1 2019 cat -rwxr-xr-x 1 root root 75588 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 63268 Mar 1 2019 chmod -rwxr-xr-x 1 root root 75588 Mar 1 2019 chown -rwxr-xr-x 1 root root 153732 Mar 1 2019 cp -rwxr-xr-x 1 root root 132820 Jan 18 2019 dash -rwxr-xr-x 1 root root 120676 Mar 1 2019 date -rwxr-xr-x 1 root root 92040 Mar 1 2019 dd -rwxr-xr-x 1 root root 100620 Mar 1 2019 df -rwxr-xr-x 1 root root 149736 Mar 1 2019 dir -rwxr-xr-x 1 root root 79412 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 34532 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 34532 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 67700 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 30112 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 206392 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 100952 Jan 6 2019 gzip -rwxr-xr-x 1 root root 21916 Sep 27 2018 hostname -rwxr-xr-x 1 root root 79752 Mar 1 2019 ln -rwxr-xr-x 1 root root 55400 Jul 27 2018 login -rwxr-xr-x 1 root root 149736 Mar 1 2019 ls -rwxr-xr-x 1 root root 112032 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 87972 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 79748 Mar 1 2019 mknod -rwxr-xr-x 1 root root 46916 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 42348 Jan 10 2019 more -rwsr-xr-x 1 root root 50592 Jan 10 2019 mount -rwxr-xr-x 1 root root 13724 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 157832 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38660 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 46852 Mar 1 2019 readlink -rwxr-xr-x 1 root root 75588 Mar 1 2019 rm -rwxr-xr-x 1 root root 42756 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 22276 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Oct 25 02:58 sh -> bash lrwxrwxrwx 1 root root 4 Oct 21 22:27 sh.distrib -> dash -rwxr-xr-x 1 root root 34532 Mar 1 2019 sleep -rwxr-xr-x 1 root root 79652 Mar 1 2019 stty -rwsr-xr-x 1 root root 71072 Jan 10 2019 su -rwxr-xr-x 1 root root 34564 Mar 1 2019 sync -rwxr-xr-x 1 root root 504024 Apr 24 2019 tar -rwxr-xr-x 1 root root 13860 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 104292 Mar 1 2019 touch -rwxr-xr-x 1 root root 34532 Mar 1 2019 true -rwxr-xr-x 1 root root 17768 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 30108 Jan 10 2019 umount -rwxr-xr-x 1 root root 34532 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 149736 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34208 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/6573/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 (>= 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 ... 19234 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 91.7 MB of archives. After unpacking 283 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 libpython2.7-minimal i386 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main i386 python2.7-minimal i386 2.7.16-2+deb10u1 [1381 kB] Get: 9 http://deb.debian.org/debian buster/main i386 python2-minimal i386 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main i386 python-minimal i386 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main i386 libssl1.1 i386 1.1.1d-0+deb10u3 [1537 kB] Get: 12 http://deb.debian.org/debian buster/main i386 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 libexpat1 i386 2.2.6-2+deb10u1 [104 kB] Get: 14 http://deb.debian.org/debian buster/main i386 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main i386 libreadline7 i386 7.0-5 [156 kB] Get: 16 http://deb.debian.org/debian buster/main i386 libpython2.7-stdlib i386 2.7.16-2+deb10u1 [1934 kB] Get: 17 http://deb.debian.org/debian buster/main i386 python2.7 i386 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libpython2-stdlib i386 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main i386 libpython-stdlib i386 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main i386 python2 i386 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main i386 python i386 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 libpython3.7-minimal i386 3.7.3-2+deb10u2 [590 kB] Get: 23 http://deb.debian.org/debian buster/main i386 python3.7-minimal i386 3.7.3-2+deb10u2 [1746 kB] Get: 24 http://deb.debian.org/debian buster/main i386 python3-minimal i386 3.7.3-1 [36.6 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libmpdec2 i386 2.4.2-2 [83.2 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libpython3.7-stdlib i386 3.7.3-2+deb10u2 [1751 kB] Get: 27 http://deb.debian.org/debian buster/main i386 python3.7 i386 3.7.3-2+deb10u2 [330 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libpython3-stdlib i386 3.7.3-1 [20.0 kB] Get: 29 http://deb.debian.org/debian buster/main i386 python3 i386 3.7.3-1 [61.5 kB] Get: 30 http://deb.debian.org/debian buster/main i386 sgml-base all 1.29 [14.8 kB] Get: 31 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 33 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 34 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 35 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 36 http://deb.debian.org/debian buster/main i386 ucf all 3.0038+nmu1 [69.0 kB] Get: 37 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 38 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 39 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 40 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 41 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 42 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 43 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 44 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 45 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 46 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 47 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 48 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 49 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 50 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 51 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 52 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 53 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 54 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 55 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 56 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 57 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 58 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 59 http://deb.debian.org/debian buster/main i386 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 60 http://deb.debian.org/debian buster/main i386 python3-distutils all 3.7.3-1 [142 kB] Get: 61 http://deb.debian.org/debian buster/main i386 dh-python all 3.20190308 [99.3 kB] Get: 62 http://deb.debian.org/debian buster/main i386 xml-core all 0.18+nmu1 [23.8 kB] Get: 63 http://deb.debian.org/debian buster/main i386 sgml-data all 2.0.11 [179 kB] Get: 64 http://deb.debian.org/debian buster/main i386 docbook-xml all 4.5-8 [84.7 kB] Get: 65 http://deb.debian.org/debian buster/main i386 docbook-xsl all 1.79.1+dfsg-2 [1249 kB] Get: 66 http://deb.debian.org/debian buster/main i386 dos2unix i386 7.4.0-1 [392 kB] Get: 67 http://deb.debian.org/debian buster/main i386 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 68 http://deb.debian.org/debian buster/main i386 fontconfig-config all 2.13.1-2 [280 kB] Get: 69 http://deb.debian.org/debian buster/main i386 libgfortran5 i386 8.3.0-6 [549 kB] Get: 70 http://deb.debian.org/debian buster/main i386 libgfortran-8-dev i386 8.3.0-6 [603 kB] Get: 71 http://deb.debian.org/debian buster/main i386 gfortran-8 i386 8.3.0-6 [9465 kB] Get: 72 http://deb.debian.org/debian buster/main i386 gfortran i386 4:8.3.0-1 [1432 B] Get: 73 http://deb.debian.org/debian buster/main i386 libblas3 i386 3.8.0-2 [142 kB] Get: 74 http://deb.debian.org/debian buster/main i386 libpng16-16 i386 1.6.36-6 [301 kB] Get: 75 http://deb.debian.org/debian buster/main i386 libfreetype6 i386 2.9.1-3+deb10u1 [395 kB] Get: 76 http://deb.debian.org/debian buster/main i386 libfontconfig1 i386 2.13.1-2 [357 kB] Get: 77 http://deb.debian.org/debian buster/main i386 libpixman-1-0 i386 0.36.0-1 [541 kB] Get: 78 http://deb.debian.org/debian buster/main i386 libxau6 i386 1:1.0.8-1+b2 [20.3 kB] Get: 79 http://deb.debian.org/debian buster/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 80 http://deb.debian.org/debian buster/main i386 libxcb1 i386 1.13.1-2 [141 kB] Get: 81 http://deb.debian.org/debian buster/main i386 libx11-data all 2:1.6.7-1+deb10u1 [294 kB] Get: 82 http://deb.debian.org/debian buster/main i386 libx11-6 i386 2:1.6.7-1+deb10u1 [778 kB] Get: 83 http://deb.debian.org/debian buster/main i386 libxcb-render0 i386 1.13.1-2 [110 kB] Get: 84 http://deb.debian.org/debian buster/main i386 libxcb-shm0 i386 1.13.1-2 [99.4 kB] Get: 85 http://deb.debian.org/debian buster/main i386 libxext6 i386 2:1.3.3-1+b2 [55.2 kB] Get: 86 http://deb.debian.org/debian buster/main i386 libxrender1 i386 1:0.9.10-1 [34.1 kB] Get: 87 http://deb.debian.org/debian buster/main i386 libcairo2 i386 1.16.0-4 [744 kB] Get: 88 http://deb.debian.org/debian buster/main i386 libexpat1-dev i386 2.2.6-2+deb10u1 [156 kB] Get: 89 http://deb.debian.org/debian buster/main i386 liblapack3 i386 3.8.0-2 [1974 kB] Get: 90 http://deb.debian.org/debian buster/main i386 libopenbabel5 i386 2.4.1+dfsg-3 [3144 kB] Get: 91 http://deb.debian.org/debian buster/main i386 libpython2.7 i386 2.7.16-2+deb10u1 [1059 kB] Get: 92 http://deb.debian.org/debian buster/main i386 libpython2.7-dev i386 2.7.16-2+deb10u1 [31.4 MB] Get: 93 http://deb.debian.org/debian buster/main i386 libpython2-dev i386 2.7.16-1 [20.9 kB] Get: 94 http://deb.debian.org/debian buster/main i386 libpython-dev i386 2.7.16-1 [20.9 kB] Get: 95 http://deb.debian.org/debian buster/main i386 libxml2-utils i386 2.9.4+dfsg1-7+b3 [100 kB] Get: 96 http://deb.debian.org/debian buster/main i386 libxslt1.1 i386 1.1.32-2.2~deb10u1 [248 kB] Get: 97 http://deb.debian.org/debian buster/main i386 openbabel i386 2.4.1+dfsg-3 [129 kB] Get: 98 http://deb.debian.org/debian buster/main i386 python2.7-dev i386 2.7.16-2+deb10u1 [295 kB] Get: 99 http://deb.debian.org/debian buster/main i386 python2-dev i386 2.7.16-1 [1208 B] Get: 100 http://deb.debian.org/debian buster/main i386 python-dev i386 2.7.16-1 [1184 B] Get: 101 http://deb.debian.org/debian buster/main i386 python-pkg-resources all 40.8.0-1 [182 kB] Get: 102 http://deb.debian.org/debian buster/main i386 python-numpy i386 1:1.16.2-1 [2096 kB] Get: 103 http://deb.debian.org/debian buster/main i386 scons all 3.0.1-2 [538 kB] Get: 104 http://deb.debian.org/debian buster/main i386 swig3.0 i386 3.0.12-2 [1456 kB] Get: 105 http://deb.debian.org/debian buster/main i386 swig i386 3.0.12-2 [310 kB] Get: 106 http://deb.debian.org/debian buster/main i386 xsltproc i386 1.1.32-2.2~deb10u1 [122 kB] Get: 107 http://deb.debian.org/debian buster/main i386 xmlto i386 0.0.28-2.1 [33.9 kB] Fetched 91.7 MB in 12s (7537 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19234 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... 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Preparing to unpack .../python3-minimal_3.7.3-1_i386.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package libmpdec2:i386. Preparing to unpack .../libmpdec2_2.4.2-2_i386.deb ... Unpacking libmpdec2:i386 (2.4.2-2) ... Selecting previously unselected package libpython3.7-stdlib:i386. Preparing to unpack .../libpython3.7-stdlib_3.7.3-2+deb10u2_i386.deb ... Unpacking libpython3.7-stdlib:i386 (3.7.3-2+deb10u2) ... Selecting previously unselected package python3.7. Preparing to unpack .../python3.7_3.7.3-2+deb10u2_i386.deb ... Unpacking python3.7 (3.7.3-2+deb10u2) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../libpython3-stdlib_3.7.3-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... Selecting previously unselected package python3. (Reading database ... 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Setting up libpython3.7-stdlib:i386 (3.7.3-2+deb10u2) ... Setting up libxcb1:i386 (1.13.1-2) ... Setting up swig (3.0.12-2) ... Setting up libtool (2.4.6-9) ... Setting up libxcb-render0:i386 (1.13.1-2) ... Setting up gfortran-8 (8.3.0-6) ... Setting up m4 (1.4.18-2) ... Setting up libxcb-shm0:i386 (1.13.1-2) ... Setting up gfortran (4:8.3.0-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libpython2.7-stdlib:i386 (2.7.16-2+deb10u1) ... Setting up libblas3:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libfreetype6:i386 (2.9.1-3+deb10u1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:i386 (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up xml-core (0.18+nmu1) ... Setting up libxslt1.1:i386 (1.1.32-2.2~deb10u1) ... Setting up libx11-6:i386 (2:1.6.7-1+deb10u1) ... Setting up libxml2-utils (2.9.4+dfsg1-7+b3) ... Setting up libpython3-stdlib:i386 (3.7.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.3-2+deb10u2) ... Setting up libpython2.7:i386 (2.7.16-2+deb10u1) ... Setting up liblapack3:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up libpython2.7-dev:i386 (2.7.16-2+deb10u1) ... Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libxrender1:i386 (1:0.9.10-1) ... Setting up libpython2-stdlib:i386 (2.7.16-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up xsltproc (1.1.32-2.2~deb10u1) ... Setting up libxext6:i386 (2:1.3.3-1+b2) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:i386 (2.7.16-1) ... Setting up libpython2-dev:i386 (2.7.16-1) ... Setting up libfontconfig1:i386 (2.13.1-2) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python (2.7.16-1) ... Setting up python2.7-dev (2.7.16-2+deb10u1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up python2-dev (2.7.16-1) ... Setting up python-pkg-resources (40.8.0-1) ... Setting up po-debconf (1.0.21) ... Setting up libcairo2:i386 (1.16.0-4) ... Setting up libpython-dev:i386 (2.7.16-1) ... Setting up scons (3.0.1-2) ... Setting up python-dev (2.7.16-1) ... Setting up python-numpy (1:1.16.2-1) ... Setting up libopenbabel5 (2.4.1+dfsg-3) ... Setting up openbabel (2.4.1+dfsg-3) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for sgml-base (1.29) ... Setting up docbook-xsl (1.79.1+dfsg-2) ... Setting up sgml-data (2.0.11) ... Processing triggers for sgml-base (1.29) ... Setting up docbook-xml (4.5-8) ... Processing triggers for sgml-base (1.29) ... 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:/i/capture/the/path" HOME="/nonexistent/second-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 i386 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-dbgsym' in '../pdb2pqr-dbgsym_2.1.1+dfsg-5_i386.deb'. 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_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pdb2pqr_2.1.1+dfsg-5_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) I: copying local configuration I: user script /srv/workspace/pbuilder/6573/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/6573/tmp/hooks/B01_cleanup finished 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/6573 and its subdirectories I: Current time: Sun Oct 25 03:02:12 +14 2020 I: pbuilder-time-stamp: 1603544532