pdb2pqr →
2.1.1+dfsg-1 →
armhf → 2016-05-13 12:10:50
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on testbuildd.raspbian.org
+==============================================================================+
| pdb2pqr 2.1.1+dfsg-1 (armhf) 13 May 2016 11:54 |
+==============================================================================+
Package: pdb2pqr
Version: 2.1.1+dfsg-1
Source Version: 2.1.1+dfsg-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/pdb2pqr-ACxgab/pdb2pqr-2.1.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pdb2pqr-ACxgab' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-136c1d77-307e-4302-b148-4468d370f59e' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8961 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.0 MB]
Fetched 20.0 MB in 24s (827 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'pdb2pqr' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/pdb2pqr.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/pdb2pqr.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 5204 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main pdb2pqr 2.1.1+dfsg-1 (dsc) [2141 B]
Get:2 http://172.17.0.1/private stretch-staging/main pdb2pqr 2.1.1+dfsg-1 (tar) [5191 kB]
Get:3 http://172.17.0.1/private stretch-staging/main pdb2pqr 2.1.1+dfsg-1 (diff) [10.4 kB]
Fetched 5204 kB in 1s (2803 kB/s)
Download complete and in download only mode
Check architectures
-------------------
Check dependencies
------------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-7BD4Jq/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-7BD4Jq/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-7BD4Jq/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-7BD4Jq/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-7BD4Jq/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-7BD4Jq/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-7BD4Jq/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-7BD4Jq/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-7BD4Jq/apt_archive ./ Packages [527 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-7BD4Jq/apt_archive/./Release.gpg: Signature by key 085A60275B95EE7E758335885FBC947B34E39F26 uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded.
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After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-7BD4Jq/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
Merged Build-Depends: debhelper (>= 9), gfortran, swig, xmlto, openbabel, python-dev, python-numpy, scons, dos2unix
Filtered Build-Depends: debhelper (>= 9), gfortran, swig, xmlto, openbabel, python-dev, python-numpy, scons, dos2unix
dpkg-deb: building package 'sbuild-build-depends-pdb2pqr-dummy' in '/<<BUILDDIR>>/resolver-kZrvxh/apt_archive/sbuild-build-depends-pdb2pqr-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-kZrvxh/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-kZrvxh/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-kZrvxh/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-kZrvxh/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-kZrvxh/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-kZrvxh/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-kZrvxh/apt_archive ./ Sources [259 B]
Get:5 file:/<<BUILDDIR>>/resolver-kZrvxh/apt_archive ./ Packages [578 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-kZrvxh/apt_archive/./Release.gpg: Signature by key 085A60275B95EE7E758335885FBC947B34E39F26 uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install pdb2pqr build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism docbook-xml docbook-xsl dos2unix file
fontconfig-config fonts-dejavu-core gcc-6-base gettext gettext-base gfortran
gfortran-5 groff-base intltool-debian libarchive-zip-perl libblas-common
libblas3 libbsd0 libcairo2 libcroco3 libexpat1 libexpat1-dev libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6
libgfortran-5-dev libgfortran3 libglib2.0-0 libicu55 liblapack3 libmagic1
libopenbabel4v5 libpipeline1 libpixman-1-0 libpython-dev libpython-stdlib
libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib
libsigsegv2 libsqlite3-0 libssl1.0.2 libtimedate-perl libtool libunistring0
libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6
libxext6 libxml2 libxml2-utils libxrender1 libxslt1.1 m4 man-db mime-support
openbabel po-debconf python python-dev python-minimal python-numpy python2.7
python2.7-dev python2.7-minimal scons sgml-base sgml-data swig swig3.0 ucf
xml-core xmlto xsltproc
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make docbook docbook-dsssl docbook-defguide dbtoepub
docbook-xsl-doc-html | docbook-xsl-doc-pdf | docbook-xsl-doc-text
| docbook-xsl-doc docbook-xsl-saxon fop libsaxon-java libxalan2-java
libxslthl-java xalan gettext-doc libasprintf-dev libgettextpo-dev
gfortran-doc gfortran-5-doc libgfortran3-dbg groff libtool-doc gcj-jdk less
www-browser libmail-box-perl python-doc python-tk python-nose
python-numpy-dbg python-numpy-doc python2.7-doc binfmt-support sgml-base-doc
perlsgml w3-recs opensp swig-doc swig-examples swig3.0-examples swig3.0-doc
w3m | lynx-cur | links xmltex
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
libltdl-dev libmail-sendmail-perl dblatex | fop libpaper-utils zip
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism docbook-xml docbook-xsl dos2unix file
fontconfig-config fonts-dejavu-core gcc-6-base gettext gettext-base gfortran
gfortran-5 groff-base intltool-debian libarchive-zip-perl libblas-common
libblas3 libbsd0 libcairo2 libcroco3 libexpat1 libexpat1-dev libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6
libgfortran-5-dev libgfortran3 libglib2.0-0 libicu55 liblapack3 libmagic1
libopenbabel4v5 libpipeline1 libpixman-1-0 libpython-dev libpython-stdlib
libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib
libsigsegv2 libsqlite3-0 libssl1.0.2 libtimedate-perl libtool libunistring0
libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6
libxext6 libxml2 libxml2-utils libxrender1 libxslt1.1 m4 man-db mime-support
openbabel po-debconf python python-dev python-minimal python-numpy python2.7
python2.7-dev python2.7-minimal sbuild-build-depends-pdb2pqr-dummy scons
sgml-base sgml-data swig swig3.0 ucf xml-core xmlto xsltproc
0 upgraded, 88 newly installed, 0 to remove and 14 not upgraded.
Need to get 90.7 MB/90.7 MB of archives.
After this operation, 288 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-kZrvxh/apt_archive ./ sbuild-build-depends-pdb2pqr-dummy 0.invalid.0 [818 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.11-8 [381 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.11-8 [1161 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-1 [40.0 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.1.1-1 [60.4 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.12.2-1 [464 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libssl1.0.2 armhf 1.0.2h-1 [889 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.11-8 [1818 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.11-8 [269 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-1 [19.5 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-1 [150 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [24.9 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.11.1-1 [40.9 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.3-1 [128 kB]
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Get:27 http://172.17.0.1/private stretch-staging/main armhf gcc-6-base armhf 6.1.1-1+rpi1 [170 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libpython2.7 armhf 2.7.11-8 [907 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf ucf all 3.0036 [70.2 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.7-2 [424 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.0-1 [2540 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.57-1 [95.1 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
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Get:51 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160403 [800 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf xml-core all 0.13+nmu2 [24.2 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf sgml-data all 2.0.10 [181 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf docbook-xml all 4.5-7.3 [83.3 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf docbook-xsl all 1.79.1+dfsg-1 [1249 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf fonts-dejavu-core all 2.35-1 [1064 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf fontconfig-config all 2.11.0-6.4 [271 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.1.1-1+rpi1 [166 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libgfortran-5-dev armhf 5.3.1-14 [182 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf gfortran-5 armhf 5.3.1-14 [23.7 MB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf gfortran armhf 4:5.3.1-1+rpi1 [1362 B]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.6.0-2 [13.5 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.6.0-2 [110 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libfreetype6 armhf 2.6.3-3 [384 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1 armhf 2.11.0-6.4 [313 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libpixman-1-0 armhf 0.33.6-1 [454 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libxcb-render0 armhf 1.11.1-1 [17.0 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libxcb-shm0 armhf 1.11.1-1 [11.5 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libxrender1 armhf 1:0.9.9-2 [28.9 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libcairo2 armhf 1.14.6-1 [688 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libexpat1-dev armhf 2.1.1-1 [117 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.6.0-2 [1382 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf libopenbabel4v5 armhf 2.3.2+dfsg-2.2+b1 [2475 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-dev armhf 2.7.11-8 [27.1 MB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libpython-dev armhf 2.7.11-1 [19.6 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libxml2-utils armhf 2.9.3+dfsg1-1 [101 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf libxslt1.1 armhf 1.1.28-2.1 [211 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf openbabel armhf 2.3.2+dfsg-2.2+b1 [250 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf python2.7-dev armhf 2.7.11-8 [276 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf python-dev armhf 2.7.11-1 [1138 B]
Get:82 http://172.17.0.1/private stretch-staging/main armhf python-numpy armhf 1:1.11.0-1 [1595 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf scons all 2.5.0-1 [525 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf swig3.0 armhf 3.0.7-2 [1190 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf swig armhf 3.0.7-2 [298 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf xsltproc armhf 1.1.28-2.1 [118 kB]
Get:87 http://172.17.0.1/private stretch-staging/main armhf xmlto armhf 0.0.28-0.1 [31.8 kB]
Get:88 http://172.17.0.1/private stretch-staging/main armhf dos2unix armhf 6.0.4-1 [75.9 kB]
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W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-14 gcc-5_5.3.1-14 libc6-dev_2.22-7 libstdc++-5-dev_5.3.1-14 libstdc++6_5.3.1-14 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.114 apt_1.2.11 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.28-1 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-14 dash_0.5.8-2.2 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160403 debianutils_4.7 dh-autoreconf_12 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.123-1 docbook-xml_4.5-7.3 docbook-xsl_1.79.1+dfsg-1 dos2unix_6.0.4-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.43~WIP.2016.03.15-2 e2fsprogs_1.43~WIP.2016.03.15-2 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 fontconfig-config_2.11.0-6.4 fonts-dejavu-core_2.35-1 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-14 gcc_4:5.3.1-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5_5.3.1-14 gcc-5-base_5.3.1-14 gcc-6-base_6.1.1-1+rpi1 gettext_0.19.7-2 gettext-base_0.19.7-2 gfortran_4:5.3.1-1+rpi1 gfortran-5_5.3.1-14 gnupg_1.4.20-6 gpgv_1.4.20-6 grep_2.25-1 groff-base_1.22.3-7 gzip_1.6-5 hostname_3.17 init_1.31 init-system-helpers_1.31 initscripts_2.88dsf-59.3 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-8+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10-4 libapt-pkg5.0_1.2.11 libarchive-zip-perl_1.57-1 libasan2_5.3.1-14 libatomic1_5.3.1-14 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libblas-common_3.6.0-2 libblas3_3.6.0-2 libblkid1_2.28-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.22-7 libc-dev-bin_2.22-7 libc6_2.22-7 libc6-dev_2.22-7 libcairo2_1.14.6-1 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-14 libcomerr2_1.43~WIP.2016.03.15-2 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.209 libdevmapper1.02.1_2:1.02.123-1 libdpkg-perl_1.18.4 libdrm2_2.4.67-1 libexpat1_2.1.1-1 libexpat1-dev_2.1.1-1 libfakeroot_1.20.2-1 libfdisk1_2.28-1 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libfontconfig1_2.11.0-6.4 libfreetype6_2.6.3-3 libgc1c2_1:7.4.2-7.4 libgcc-5-dev_5.3.1-14 libgcc1_1:5.3.1-14 libgcrypt20_1.7.0-2 libgdbm3_1.8.3-13.1 libgfortran-5-dev_5.3.1-14 libgfortran3_6.1.1-1+rpi1 libglib2.0-0_2.48.0-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-14 libgpg-error0_1.22-1 libicu55_55.1-7 libisl15_0.16.1-1 libklibc_2.0.4-8+rpi1 libkmod2_22-1.1 liblapack3_3.6.0-2 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.28-1 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160319-1 libncursesw5_6.0+20160319-1 libopenbabel4v5_2.3.2+dfsg-2.2+b1 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpcre3_2:8.38-3.1 libperl5.22_5.22.2-1 libpipeline1_1.4.1-2 libpixman-1-0_0.33.6-1 libpng12-0_1.2.54-6 libprocps5_2:3.3.11-3 libpython-dev_2.7.11-1 libpython-stdlib_2.7.11-1 libpython2.7_2.7.11-8 libpython2.7-dev_2.7.11-8 libpython2.7-minimal_2.7.11-8 libpython2.7-stdlib_2.7.11-8 libreadline6_6.3-8+b3 libseccomp2_2.3.0-1 libselinux1_2.5-2 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28-1 libsqlite3-0_3.12.2-1 libss2_1.43~WIP.2016.03.15-2 libssl1.0.2_1.0.2h-1 libstdc++-5-dev_5.3.1-14 libstdc++6_5.3.1-14 libsystemd0_229-5 libtext-charwidth-perl_0.04-7+b6 libtext-iconv-perl_1.7-5+b7 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160319-1 libtool_2.4.6-0.1 libubsan0_5.3.1-14 libudev1_229-5 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.28-1 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libxau6_1:1.0.8-1 libxcb-render0_1.11.1-1 libxcb-shm0_1.11.1-1 libxcb1_1.11.1-1 libxdmcp6_1:1.1.2-1.1 libxext6_2:1.3.3-1 libxml2_2.9.3+dfsg1-1 libxml2-utils_2.9.3+dfsg1-1 libxrender1_1:0.9.9-2 libxslt1.1_1.1.28-2.1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.05-1 mawk_1.3.3-17 mime-support_3.60 mount_2.28-1 multiarch-support_2.22-7 nano_2.5.3-3 ncurses-base_6.0+20160319-1 ncurses-bin_6.0+20160319-1 openbabel_2.3.2+dfsg-2.2+b1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-1 perl-base_5.22.2-1 perl-modules-5.22_5.22.2-1 po-debconf_1.0.19 procps_2:3.3.11-3 python_2.7.11-1 python-dev_2.7.11-1 python-minimal_2.7.11-1 python-numpy_1:1.11.0-1 python2.7_2.7.11-8 python2.7-dev_2.7.11-8 python2.7-minimal_2.7.11-8 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pdb2pqr-dummy_0.invalid.0 scons_2.5.0-1 sed_4.2.2-7.1 sensible-utils_0.0.9 sgml-base_1.26+nmu4 sgml-data_2.0.10 startpar_0.59-3 swig_3.0.7-2 swig3.0_3.0.7-2 systemd_229-5 systemd-sysv_229-5 sysv-rc_2.88dsf-59.3 sysvinit-utils_2.88dsf-59.3 tar_1.28-2.1 tzdata_2016d-2 ucf_3.0036 udev_229-5 util-linux_2.28-1 xml-core_0.13+nmu2 xmlto_0.0.28-0.1 xsltproc_1.1.28-2.1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat May 7 21:57:42 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./pdb2pqr_2.1.1+dfsg-1.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-1.debian.tar.xz
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
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-136c1d77-307e-4302-b148-4468d370f59e
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package pdb2pqr
dpkg-buildpackage: source version 2.1.1+dfsg-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build pdb2pqr-2.1.1+dfsg
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean --with python2
dh_testdir
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/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 '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_clean
debian/rules build-arch
dh build-arch --with python2
dh_testdir -a
dh_update_autotools_config -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_auto_configure
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 -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:1777:0,
from /usr/include/python2.7/numpy/ndarrayobject.h:18,
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:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
g++ -o pdb2pka/substruct/Algorithms.so -shared -Wl,-Bsymbolic -Wl,-soname=Algorithms.so pdb2pka/substruct/Algorithms.os -L/usr/lib -lpython2.7
g++ -o pdb2pka/pMC_mult.os -c -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 -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 -shared -Wl,-Bsymbolic -Wl,-soname=_pMC_mult.so 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.
( 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 )
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_auto_build -a
dh_auto_test -a
fakeroot debian/rules binary-arch
dh binary-arch --with python2
dh_testroot -a
dh_prep -a
dh_installdirs -a
dh_auto_install -a
debian/rules override_dh_install-arch
make[1]: Entering directory '/<<BUILDDIR>>/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 '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_installchangelogs ChangeLog.md
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
debian/rules override_dh_installman-arch
make[1]: Entering directory '/<<BUILDDIR>>/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 '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_python2 -a
W: dh_python2:479: Please add dh-python package to Build-Depends
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms-arch
make[1]: Entering directory '/<<BUILDDIR>>/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 '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/pdb2pqr/usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.so contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/pdb2pqr/usr/lib/pdb2pqr/pdb2pka/_pMC_mult.so contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'pdb2pqr-dbgsym' in '../pdb2pqr-dbgsym_2.1.1+dfsg-1_armhf.deb'.
dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_2.1.1+dfsg-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../pdb2pqr_2.1.1+dfsg-1_armhf.changes
dpkg-genchanges: warning: package pdb2pqr-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build pdb2pqr-2.1.1+dfsg
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160513-1207
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pdb2pqr_2.1.1+dfsg-1_armhf.changes:
-----------------------------------
Format: 1.8
Date: Sat, 07 May 2016 23:56:17 +0200
Source: pdb2pqr
Binary: pdb2pqr pdb2pqr-doc
Architecture: armhf
Version: 2.1.1+dfsg-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
pdb2pqr - Preparation of protein structures for electrostatics calculations
pdb2pqr-doc - example files accompanying pdb2pqr
Changes:
pdb2pqr (2.1.1+dfsg-1) unstable; urgency=medium
.
* New upstream version
* Add new options to d/watch
* cme fix dpkg-control
* drop wrapper and use links instead
* fix interpreter lines by dos2unix
Checksums-Sha1:
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959e0cc1912007805ccb3417b9e5f0adefc14ad3 348808 pdb2pqr_2.1.1+dfsg-1_armhf.deb
Checksums-Sha256:
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d4299364e0a1643dcdae4c09a059d33106b32077af7f6a1a421ee90bc0d2ff39 348808 pdb2pqr_2.1.1+dfsg-1_armhf.deb
Files:
a64a035d9eb224ff3ed58eef3c543598 35176 debug extra pdb2pqr-dbgsym_2.1.1+dfsg-1_armhf.deb
11462163a2f4766dad8d08bc2e57de9b 348808 science optional pdb2pqr_2.1.1+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
pdb2pqr-dbgsym_2.1.1+dfsg-1_armhf.deb
-------------------------------------
new debian package, version 2.0.
size 35176 bytes: control archive=547 bytes.
458 bytes, 13 lines control
212 bytes, 2 lines md5sums
Package: pdb2pqr-dbgsym
Source: pdb2pqr
Version: 2.1.1+dfsg-1
Architecture: armhf
Maintainer: Debian Med <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 263
Depends: pdb2pqr (= 2.1.1+dfsg-1)
Section: debug
Priority: extra
Homepage: http://pdb2pqr.poissonboltzmann.org/pdb2pqr/
Description: Debug symbols for pdb2pqr
Auto-Built-Package: debug-symbols
Build-Ids: 328b3e54b536f873759a16aef259e2cfba83073d 7efeaa4137cb1b4ed2e02c88d0c990297cb04331
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pdb2pqr_2.1.1+dfsg-1_armhf.deb
------------------------------
new debian package, version 2.0.
size 348808 bytes: control archive=4715 bytes.
1357 bytes, 28 lines control
8965 bytes, 122 lines md5sums
182 bytes, 9 lines * postinst #!/bin/sh
251 bytes, 14 lines * prerm #!/bin/sh
Package: pdb2pqr
Version: 2.1.1+dfsg-1
Architecture: armhf
Maintainer: Debian Med <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2700
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libpython2.7 (>= 2.7), libstdc++6 (>= 5.2), python:any (>= 2.6.6-7~), python2.7:any, python-numpy
Suggests: apbs
Enhances: autodocktools
Replaces: propka
Provides: propka
Section: science
Priority: optional
Homepage: http://pdb2pqr.poissonboltzmann.org/pdb2pqr/
Description: Preparation of protein structures for electrostatics calculations
PDB2PQR is a Python software package that automates many of the common
tasks of preparing structures for continuum electrostatics calculations.
It thus provides a platform-independent utility for converting protein files
in PDB format to PQR format. These tasks include:
* Adding a limited number of missing heavy atoms to biomolecular structures
* Determining side-chain pKas
* Placing missing hydrogens
* Optimizing the protein for favorable hydrogen bonding
* Assigning charge and radius parameters from a variety of force fields
.
This package also includes PropKa, a tool to modify the protonation state of
protein structures in the Protein Data Bank (PDB) format to match a given pKa
value. It can also be used to refine NMR structures, which often yield
inaccurate pKa values for some residues.
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
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| Summary |
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Build Architecture: armhf
Build-Space: 50972
Build-Time: 112
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 641
Job: pdb2pqr_2.1.1+dfsg-1
Machine Architecture: armhf
Package: pdb2pqr
Package-Time: 809
Source-Version: 2.1.1+dfsg-1
Space: 50972
Status: successful
Version: 2.1.1+dfsg-1
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Finished at 20160513-1207
Build needed 00:13:29, 50972k disc space