I: pbuilder: network access will be disabled during build
I: Current time: Sun Apr 30 22:09:09 +14 2023
I: pbuilder-time-stamp: 1682842149
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.3knFJbSG/trustedkeys.kbx': General error
gpgv: Signature made Sun Feb 20 08:48:53 2022 +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-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/34026/tmp/hooks/D01_modify_environment starting
debug: Running on ionos16-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/34026/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/34026/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]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
BASH_VERSION='5.1.4(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,-fixfilepath parallel=15'
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=cf10ce6926714226a9d4c397919a969a
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=34026
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.GzvVW2do5d/pbuilderrc_ZKfq --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.GzvVW2do5d/b2 --logfile b2/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-14
UID=0
USER=root
_='I: set'
http_proxy=http://85.184.249.68:3128
I: uname -a
Linux i-capture-the-hostname 5.10.0-12-amd64 #1 SMP Debian 5.10.103-1 (2022-03-07) x86_64 GNU/Linux
I: ls -l /bin
total 5776
-rwxr-xr-x 1 root root 1367848 Aug 5 2021 bash
-rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2
-rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep
-rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2
-rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore
-rwxr-xr-x 1 root root 38824 Sep 23 2020 cat
-rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp
-rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod
-rwxr-xr-x 1 root root 75752 Sep 23 2020 chown
-rwxr-xr-x 1 root root 157960 Sep 23 2020 cp
-rwxr-xr-x 1 root root 128724 Dec 11 2020 dash
-rwxr-xr-x 1 root root 124904 Sep 23 2020 date
-rwxr-xr-x 1 root root 92172 Sep 23 2020 dd
-rwxr-xr-x 1 root root 100752 Sep 23 2020 df
-rwxr-xr-x 1 root root 153964 Sep 23 2020 dir
-rwxr-xr-x 1 root root 83644 Jan 21 2022 dmesg
lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname
-rwxr-xr-x 1 root root 34664 Sep 23 2020 echo
-rwxr-xr-x 1 root root 28 Nov 10 2020 egrep
-rwxr-xr-x 1 root root 34664 Sep 23 2020 false
-rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep
-rwxr-xr-x 1 root root 71928 Jan 21 2022 findmnt
-rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount
-rwxr-xr-x 1 root root 210488 Nov 10 2020 grep
-rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip
-rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe
-rwxr-xr-x 1 root root 100952 Mar 3 2021 gzip
-rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname
-rwxr-xr-x 1 root root 83980 Sep 23 2020 ln
-rwxr-xr-x 1 root root 55572 Feb 8 2020 login
-rwxr-xr-x 1 root root 153964 Sep 23 2020 ls
-rwxr-xr-x 1 root root 153124 Jan 21 2022 lsblk
-rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir
-rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod
-rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp
-rwxr-xr-x 1 root root 58920 Jan 21 2022 more
-rwsr-xr-x 1 root root 50720 Jan 21 2022 mount
-rwxr-xr-x 1 root root 13856 Jan 21 2022 mountpoint
-rwxr-xr-x 1 root root 157996 Sep 23 2020 mv
lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd
lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash
-rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink
-rwxr-xr-x 1 root root 75720 Sep 23 2020 rm
-rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir
-rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts
-rwxr-xr-x 1 root root 125036 Dec 23 2018 sed
lrwxrwxrwx 1 root root 4 Apr 30 22:09 sh -> bash
lrwxrwxrwx 1 root root 4 Apr 24 05:46 sh.distrib -> dash
-rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep
-rwxr-xr-x 1 root root 83880 Sep 23 2020 stty
-rwsr-xr-x 1 root root 79396 Jan 21 2022 su
-rwxr-xr-x 1 root root 34696 Sep 23 2020 sync
-rwxr-xr-x 1 root root 602584 Feb 17 2021 tar
-rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile
-rwxr-xr-x 1 root root 108520 Sep 23 2020 touch
-rwxr-xr-x 1 root root 34664 Sep 23 2020 true
-rwxr-xr-x 1 root root 17768 Feb 27 2021 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Jan 21 2022 umount
-rwxr-xr-x 1 root root 34664 Sep 23 2020 uname
-rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress
-rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir
-rwxr-xr-x 1 root root 63024 Jan 21 2022 wdctl
lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat
-rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp
-rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff
-rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep
-rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep
-rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce
-rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep
-rwxr-xr-x 1 root root 2206 Mar 3 2021 zless
-rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore
-rwxr-xr-x 1 root root 4553 Mar 3 2021 znew
I: user script /srv/workspace/pbuilder/34026/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 <pbuilder-maint@lists.alioth.debian.org>
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 3s (22.9 MB/s)
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Reading package lists...
Building dependency tree...
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Building tag database...
-> Finished parsing the build-deps
I: Building the package
hostname: Name or service not known
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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 <merkys@debian.org>
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-dbgsym' in '../pdb2pqr-dbgsym_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-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: user script /srv/workspace/pbuilder/34026/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/34026/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/34026 and its subdirectories
I: Current time: Sun Apr 30 22:09:56 +14 2023
I: pbuilder-time-stamp: 1682842196