pdb2pqr →
2.0.0+dfsg-2 →
armhf → 2015-12-02 06:02:54
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-01
╔══════════════════════════════════════════════════════════════════════════════╗
║ pdb2pqr 2.0.0+dfsg-2 (armhf) 02 Dec 2015 05:47 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: pdb2pqr
Version: 2.0.0+dfsg-2
Source Version: 2.0.0+dfsg-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/pdb2pqr-56fcvd/pdb2pqr-2.0.0+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/pdb2pqr-56fcvd' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-5b5ee240-cab2-4269-918a-97fe12ac50f4' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8503 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.5 MB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
Fetched 19.0 MB in 34s (550 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
─────────
Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'pdb2pqr' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/pdb2pqr/trunk/
Need to get 1796 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main pdb2pqr 2.0.0+dfsg-2 (dsc) [2159 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main pdb2pqr 2.0.0+dfsg-2 (tar) [1784 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main pdb2pqr 2.0.0+dfsg-2 (diff) [9976 B]
Fetched 1796 kB in 0s (3972 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-YToTuP/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
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
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 20 not upgraded.
Need to get 0 B/764 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(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 ... 12030 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), gfortran, swig, xmlto, openbabel, python-dev, python-numpy, scons
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), gfortran, swig, xmlto, openbabel, python-dev, python-numpy, scons
dpkg-deb: building package 'sbuild-build-depends-pdb2pqr-dummy' in '/«BUILDDIR»/resolver-8btnsb/apt_archive/sbuild-build-depends-pdb2pqr-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install pdb2pqr build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils cpp cpp-5 debhelper dh-strip-nondeterminism docbook-xml
docbook-xsl file fontconfig-config fonts-dejavu-core g++-5 gcc gcc-5
gcc-5-base gettext gettext-base gfortran gfortran-5 groff-base
intltool-debian libarchive-zip-perl libasan2 libatomic1 libblas-common
libblas3 libcairo2 libcc1-0 libcroco3 libexpat1 libexpat1-dev libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-5-dev
libgcc1 libgfortran-5-dev libgfortran3 libglib2.0-0 libgomp1 libicu55
libisl15 liblapack3 libmagic1 libopenbabel4v5 libpipeline1 libpixman-1-0
libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev
libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libssl1.0.2
libstdc++-5-dev libstdc++6 libtimedate-perl libubsan0 libunistring0 libx11-6
libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6
libxml2 libxml2-utils libxrender1 libxslt1.1 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:
wamerican wordlist whois vacation cpp-doc gcc-5-locales 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 gcc-5-doc
libstdc++6-5-dbg gcc-multilib manpages-dev autoconf automake libtool flex
bison gdb gcc-doc libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
libasan2-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg
libmpx0-dbg libquadmath-dbg gettext-doc autopoint libasprintf-dev
libgettextpo-dev gfortran-doc gfortran-5-doc libgfortran3-dbg groff
libstdc++-5-doc 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 xmltex
Recommended packages:
curl wget lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
libmail-sendmail-perl libpaper-utils zip
The following NEW packages will be installed:
bsdmainutils debhelper dh-strip-nondeterminism docbook-xml docbook-xsl file
fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-5
groff-base intltool-debian libarchive-zip-perl libblas-common libblas3
libcairo2 libcroco3 libexpat1 libexpat1-dev libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6
libgfortran-5-dev libgfortran3 libglib2.0-0 libicu55 libisl15 liblapack3
libmagic1 libopenbabel4v5 libpipeline1 libpixman-1-0 libpython-dev
libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal
libpython2.7-stdlib libsqlite3-0 libssl1.0.2 libtimedate-perl libunistring0
libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6
libxext6 libxml2 libxml2-utils libxrender1 libxslt1.1 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
The following packages will be upgraded:
cpp cpp-5 g++-5 gcc gcc-5 gcc-5-base libasan2 libatomic1 libcc1-0
libgcc-5-dev libgcc1 libgomp1 libstdc++-5-dev libstdc++6 libubsan0
15 upgraded, 78 newly installed, 0 to remove and 5 not upgraded.
Need to get 170 MB/170 MB of archives.
After this operation, 281 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main libgomp1 armhf 5.2.1-23+rpi1+b1 [47.4 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main libatomic1 armhf 5.2.1-23+rpi1+b1 [6606 B]
Get:3 http://172.17.0.1/private/ stretch-staging/main gcc-5-base armhf 5.2.1-23+rpi1+b1 [167 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main libgcc1 armhf 1:5.2.1-23+rpi1+b1 [38.5 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libasan2 armhf 5.2.1-23+rpi1+b1 [227 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libubsan0 armhf 5.2.1-23+rpi1+b1 [84.3 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main libisl15 armhf 0.15-3 [397 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main cpp-5 armhf 5.2.1-23+rpi1+b1 [22.9 MB]
Get:9 http://172.17.0.1/private/ stretch-staging/main libcc1-0 armhf 5.2.1-23+rpi1+b1 [24.7 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main g++-5 armhf 5.2.1-23+rpi1+b1 [32.0 MB]
Get:11 http://172.17.0.1/private/ stretch-staging/main gcc-5 armhf 5.2.1-23+rpi1+b1 [22.9 MB]
Get:12 http://172.17.0.1/private/ stretch-staging/main libgcc-5-dev armhf 5.2.1-23+rpi1+b1 [449 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libstdc++-5-dev armhf 5.2.1-23+rpi1+b1 [1428 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main libstdc++6 armhf 5.2.1-23+rpi1+b1 [327 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-4 [1084 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.1-1 [23.9 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.5-1 [975 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main libpython2.7-minimal armhf 2.7.10-5+b1 [380 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main python2.7-minimal armhf 2.7.10-5+b1 [1092 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main python-minimal armhf 2.7.9-1 [40.1 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main mime-support all 3.59 [36.4 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main libexpat1 armhf 2.1.0-7 [59.8 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.2.1-3 [18.5 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main libsqlite3-0 armhf 3.9.2-1 [404 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main libssl1.0.2 armhf 1.0.2d-3 [881 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main libpython2.7-stdlib armhf 2.7.10-5+b1 [1811 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main python2.7 armhf 2.7.10-5+b1 [265 kB]
Get:29 http://172.17.0.1/private/ stretch-staging/main libpython-stdlib armhf 2.7.9-1 [19.6 kB]
Get:30 http://172.17.0.1/private/ stretch-staging/main python armhf 2.7.9-1 [151 kB]
Get:31 http://172.17.0.1/private/ stretch-staging/main libfreetype6 armhf 2.6.1-0.1 [411 kB]
Get:32 http://172.17.0.1/private/ stretch-staging/main ucf all 3.0031 [68.9 kB]
Get:33 http://172.17.0.1/private/ stretch-staging/main fonts-dejavu-core all 2.35-1 [1064 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main fontconfig-config all 2.11.0-6.3 [273 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main libfontconfig1 armhf 2.11.0-6.3 [311 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main libxdmcp6 armhf 1:1.1.2-1 [25.0 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main libxcb1 armhf 1.10-3+b1 [40.6 kB]
Get:40 http://172.17.0.1/private/ stretch-staging/main libx11-data all 2:1.6.3-1 [128 kB]
Get:41 http://172.17.0.1/private/ stretch-staging/main libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:42 http://172.17.0.1/private/ stretch-staging/main libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:43 http://172.17.0.1/private/ stretch-staging/main sgml-base all 1.26+nmu4 [14.6 kB]
Get:44 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.25-2 [250 kB]
Get:45 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.25-2 [61.2 kB]
Get:46 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.6-1 [119 kB]
Get:47 http://172.17.0.1/private/ stretch-staging/main libpython2.7 armhf 2.7.10-5+b1 [908 kB]
Get:48 http://172.17.0.1/private/ stretch-staging/main libicu55 armhf 55.1-6 [7379 kB]
Get:49 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.2+zdfsg1-4 [797 kB]
Get:50 http://172.17.0.1/private/ stretch-staging/main cpp armhf 4:5.2.1-4+rpi3 [17.9 kB]
Get:51 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.46.2-1 [2482 kB]
Get:52 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.9-1 [129 kB]
Get:53 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.6-1 [1393 kB]
Get:54 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:55 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:56 http://172.17.0.1/private/ stretch-staging/main libarchive-zip-perl all 1.53-1 [97.3 kB]
Get:57 http://172.17.0.1/private/ stretch-staging/main libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
Get:58 http://172.17.0.1/private/ stretch-staging/main libtimedate-perl all 2.3000-2 [42.2 kB]
Get:59 http://172.17.0.1/private/ stretch-staging/main dh-strip-nondeterminism all 0.014-1 [7472 B]
Get:60 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20151005 [817 kB]
Get:61 http://172.17.0.1/private/ stretch-staging/main xml-core all 0.13+nmu2 [24.2 kB]
Get:62 http://172.17.0.1/private/ stretch-staging/main sgml-data all 2.0.10 [181 kB]
Get:63 http://172.17.0.1/private/ stretch-staging/main docbook-xml all 4.5-7.3 [83.3 kB]
Get:64 http://172.17.0.1/private/ stretch-staging/main docbook-xsl all 1.78.1+dfsg-1 [2339 kB]
Get:65 http://172.17.0.1/private/ stretch-staging/main gcc armhf 4:5.2.1-4+rpi3 [5218 B]
Get:66 http://172.17.0.1/private/ stretch-staging/main libgfortran3 armhf 5.2.1-23+rpi1+b1 [154 kB]
Get:67 http://172.17.0.1/private/ stretch-staging/main libgfortran-5-dev armhf 5.2.1-23+rpi1+b1 [183 kB]
Get:68 http://172.17.0.1/private/ stretch-staging/main gfortran-5 armhf 5.2.1-23+rpi1+b1 [23.7 MB]
Get:69 http://172.17.0.1/private/ stretch-staging/main gfortran armhf 4:5.2.1-4+rpi3 [1372 B]
Get:70 http://172.17.0.1/private/ stretch-staging/main libblas-common armhf 1.2.20110419-11 [8490 B]
Get:71 http://172.17.0.1/private/ stretch-staging/main libblas3 armhf 1.2.20110419-11 [118 kB]
Get:72 http://172.17.0.1/private/ stretch-staging/main libpixman-1-0 armhf 0.33.4-1 [453 kB]
Get:73 http://172.17.0.1/private/ stretch-staging/main libxcb-render0 armhf 1.10-3+b1 [16.9 kB]
Get:74 http://172.17.0.1/private/ stretch-staging/main libxcb-shm0 armhf 1.10-3+b1 [11.4 kB]
Get:75 http://172.17.0.1/private/ stretch-staging/main libxrender1 armhf 1:0.9.9-2 [28.9 kB]
Get:76 http://172.17.0.1/private/ stretch-staging/main libcairo2 armhf 1.14.4-1 [687 kB]
Get:77 http://172.17.0.1/private/ stretch-staging/main libexpat1-dev armhf 2.1.0-7 [114 kB]
Get:78 http://172.17.0.1/private/ stretch-staging/main liblapack3 armhf 3.5.0-5 [1294 kB]
Get:79 http://172.17.0.1/private/ stretch-staging/main libopenbabel4v5 armhf 2.3.2+dfsg-2.2 [2461 kB]
Get:80 http://172.17.0.1/private/ stretch-staging/main libpython2.7-dev armhf 2.7.10-5+b1 [27.1 MB]
Get:81 http://172.17.0.1/private/ stretch-staging/main libpython-dev armhf 2.7.9-1 [19.6 kB]
Get:82 http://172.17.0.1/private/ stretch-staging/main libxml2-utils armhf 2.9.2+zdfsg1-4 [101 kB]
Get:83 http://172.17.0.1/private/ stretch-staging/main libxslt1.1 armhf 1.1.28-2.1 [211 kB]
Get:84 http://172.17.0.1/private/ stretch-staging/main openbabel armhf 2.3.2+dfsg-2.2 [249 kB]
Get:85 http://172.17.0.1/private/ stretch-staging/main python2.7-dev armhf 2.7.10-5+b1 [279 kB]
Get:86 http://172.17.0.1/private/ stretch-staging/main python-dev armhf 2.7.9-1 [1188 B]
Get:87 http://172.17.0.1/private/ stretch-staging/main python-numpy armhf 1:1.9.2-5 [1511 kB]
Get:88 http://172.17.0.1/private/ stretch-staging/main scons all 2.4.1-1 [540 kB]
Get:89 http://172.17.0.1/private/ stretch-staging/main swig3.0 armhf 3.0.7-2 [1190 kB]
Get:90 http://172.17.0.1/private/ stretch-staging/main swig armhf 3.0.7-2 [298 kB]
Get:91 http://172.17.0.1/private/ stretch-staging/main xsltproc armhf 1.1.28-2.1 [118 kB]
Get:92 http://172.17.0.1/private/ stretch-staging/main xmlto armhf 0.0.28-0.1 [31.8 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 170 MB in 40s (4194 kB/s)
(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 ... 12030 files and directories currently installed.)
Preparing to unpack .../libgomp1_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libgomp1:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../libatomic1_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libatomic1:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../gcc-5-base_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking gcc-5-base:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Processing triggers for libc-bin (2.19-22) ...
Setting up gcc-5-base:armhf (5.2.1-23+rpi1+b1) ...
(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 ... 12031 files and directories currently installed.)
Preparing to unpack .../libgcc1_1%3a5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libgcc1:armhf (1:5.2.1-23+rpi1+b1) over (1:5.2.1-23+rpi1) ...
Processing triggers for libc-bin (2.19-22) ...
Setting up libgcc1:armhf (1:5.2.1-23+rpi1+b1) ...
Processing triggers for libc-bin (2.19-22) ...
(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 ... 12031 files and directories currently installed.)
Preparing to unpack .../libasan2_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libasan2:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../libubsan0_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libubsan0:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Selecting previously unselected package libisl15:armhf.
Preparing to unpack .../libisl15_0.15-3_armhf.deb ...
Unpacking libisl15:armhf (0.15-3) ...
Preparing to unpack .../cpp-5_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking cpp-5 (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../libcc1-0_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libcc1-0:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../g++-5_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking g++-5 (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../gcc-5_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking gcc-5 (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../libgcc-5-dev_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libgcc-5-dev:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../libstdc++-5-dev_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libstdc++-5-dev:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../libstdc++6_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libstdc++6:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Processing triggers for libc-bin (2.19-22) ...
Setting up libstdc++6:armhf (5.2.1-23+rpi1+b1) ...
Processing triggers for libc-bin (2.19-22) ...
Selecting previously unselected package groff-base.
(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 ... 12037 files and directories currently installed.)
Preparing to unpack .../groff-base_1.22.3-4_armhf.deb ...
Unpacking groff-base (1.22.3-4) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../bsdmainutils_9.0.6_armhf.deb ...
Unpacking bsdmainutils (9.0.6) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../libpipeline1_1.4.1-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.4.1-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../man-db_2.7.5-1_armhf.deb ...
Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libpython2.7-minimal:armhf.
Preparing to unpack .../libpython2.7-minimal_2.7.10-5+b1_armhf.deb ...
Unpacking libpython2.7-minimal:armhf (2.7.10-5+b1) ...
Selecting previously unselected package python2.7-minimal.
Preparing to unpack .../python2.7-minimal_2.7.10-5+b1_armhf.deb ...
Unpacking python2.7-minimal (2.7.10-5+b1) ...
Selecting previously unselected package python-minimal.
Preparing to unpack .../python-minimal_2.7.9-1_armhf.deb ...
Unpacking python-minimal (2.7.9-1) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../mime-support_3.59_all.deb ...
Unpacking mime-support (3.59) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../libexpat1_2.1.0-7_armhf.deb ...
Unpacking libexpat1:armhf (2.1.0-7) ...
Selecting previously unselected package libffi6:armhf.
Preparing to unpack .../libffi6_3.2.1-3_armhf.deb ...
Unpacking libffi6:armhf (3.2.1-3) ...
Selecting previously unselected package libsqlite3-0:armhf.
Preparing to unpack .../libsqlite3-0_3.9.2-1_armhf.deb ...
Unpacking libsqlite3-0:armhf (3.9.2-1) ...
Selecting previously unselected package libssl1.0.2:armhf.
Preparing to unpack .../libssl1.0.2_1.0.2d-3_armhf.deb ...
Unpacking libssl1.0.2:armhf (1.0.2d-3) ...
Selecting previously unselected package libpython2.7-stdlib:armhf.
Preparing to unpack .../libpython2.7-stdlib_2.7.10-5+b1_armhf.deb ...
Unpacking libpython2.7-stdlib:armhf (2.7.10-5+b1) ...
Selecting previously unselected package python2.7.
Preparing to unpack .../python2.7_2.7.10-5+b1_armhf.deb ...
Unpacking python2.7 (2.7.10-5+b1) ...
Selecting previously unselected package libpython-stdlib:armhf.
Preparing to unpack .../libpython-stdlib_2.7.9-1_armhf.deb ...
Unpacking libpython-stdlib:armhf (2.7.9-1) ...
Processing triggers for libc-bin (2.19-22) ...
Setting up libpython2.7-minimal:armhf (2.7.10-5+b1) ...
Setting up python2.7-minimal (2.7.10-5+b1) ...
Setting up python-minimal (2.7.9-1) ...
Selecting previously unselected package python.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 13405 files and directories currently installed.)
Preparing to unpack .../python_2.7.9-1_armhf.deb ...
Unpacking python (2.7.9-1) ...
Selecting previously unselected package libfreetype6:armhf.
Preparing to unpack .../libfreetype6_2.6.1-0.1_armhf.deb ...
Unpacking libfreetype6:armhf (2.6.1-0.1) ...
Selecting previously unselected package ucf.
Preparing to unpack .../archives/ucf_3.0031_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0031) ...
Selecting previously unselected package fonts-dejavu-core.
Preparing to unpack .../fonts-dejavu-core_2.35-1_all.deb ...
Unpacking fonts-dejavu-core (2.35-1) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../fontconfig-config_2.11.0-6.3_all.deb ...
Unpacking fontconfig-config (2.11.0-6.3) ...
Selecting previously unselected package libfontconfig1:armhf.
Preparing to unpack .../libfontconfig1_2.11.0-6.3_armhf.deb ...
Unpacking libfontconfig1:armhf (2.11.0-6.3) ...
Selecting previously unselected package libunistring0:armhf.
Preparing to unpack .../libunistring0_0.9.3-5.2_armhf.deb ...
Unpacking libunistring0:armhf (0.9.3-5.2) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../libxau6_1%3a1.0.8-1_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.8-1) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../libxdmcp6_1%3a1.1.2-1_armhf.deb ...
Unpacking libxdmcp6:armhf (1:1.1.2-1) ...
Selecting previously unselected package libxcb1:armhf.
Preparing to unpack .../libxcb1_1.10-3+b1_armhf.deb ...
Unpacking libxcb1:armhf (1.10-3+b1) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../libx11-data_2%3a1.6.3-1_all.deb ...
Unpacking libx11-data (2:1.6.3-1) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../libx11-6_2%3a1.6.3-1_armhf.deb ...
Unpacking libx11-6:armhf (2:1.6.3-1) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../libxext6_2%3a1.3.3-1_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.3-1) ...
Selecting previously unselected package sgml-base.
Preparing to unpack .../sgml-base_1.26+nmu4_all.deb ...
Unpacking sgml-base (1.26+nmu4) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../libmagic1_1%3a5.25-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.25-2) ...
Selecting previously unselected package file.
Preparing to unpack .../file_1%3a5.25-2_armhf.deb ...
Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.6-1_armhf.deb ...
Unpacking gettext-base (0.19.6-1) ...
Selecting previously unselected package libpython2.7:armhf.
Preparing to unpack .../libpython2.7_2.7.10-5+b1_armhf.deb ...
Unpacking libpython2.7:armhf (2.7.10-5+b1) ...
Selecting previously unselected package libicu55:armhf.
Preparing to unpack .../libicu55_55.1-6_armhf.deb ...
Unpacking libicu55:armhf (55.1-6) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_armhf.deb ...
Unpacking libxml2:armhf (2.9.2+zdfsg1-4) ...
Preparing to unpack .../cpp_4%3a5.2.1-4+rpi3_armhf.deb ...
Unpacking cpp (4:5.2.1-4+rpi3) over (4:5.2.1-4+rpi2) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../libglib2.0-0_2.46.2-1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.46.2-1) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../libcroco3_0.6.9-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.9-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.6-1_armhf.deb ...
Unpacking gettext (0.19.6-1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../po-debconf_1.0.18_all.deb ...
Unpacking po-debconf (1.0.18) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../libarchive-zip-perl_1.53-1_all.deb ...
Unpacking libarchive-zip-perl (1.53-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (0.014-1) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
Unpacking libtimedate-perl (2.3000-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ...
Unpacking dh-strip-nondeterminism (0.014-1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../debhelper_9.20151005_all.deb ...
Unpacking debhelper (9.20151005) ...
Selecting previously unselected package xml-core.
Preparing to unpack .../xml-core_0.13+nmu2_all.deb ...
Unpacking xml-core (0.13+nmu2) ...
Selecting previously unselected package sgml-data.
Preparing to unpack .../sgml-data_2.0.10_all.deb ...
Unpacking sgml-data (2.0.10) ...
Selecting previously unselected package docbook-xml.
Preparing to unpack .../docbook-xml_4.5-7.3_all.deb ...
Unpacking docbook-xml (4.5-7.3) ...
Selecting previously unselected package docbook-xsl.
Preparing to unpack .../docbook-xsl_1.78.1+dfsg-1_all.deb ...
Unpacking docbook-xsl (1.78.1+dfsg-1) ...
Preparing to unpack .../gcc_4%3a5.2.1-4+rpi3_armhf.deb ...
Removing old gcc doc directory.
Unpacking gcc (4:5.2.1-4+rpi3) over (4:5.2.1-4+rpi2) ...
Selecting previously unselected package libgfortran3:armhf.
Preparing to unpack .../libgfortran3_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libgfortran3:armhf (5.2.1-23+rpi1+b1) ...
Selecting previously unselected package libgfortran-5-dev:armhf.
Preparing to unpack .../libgfortran-5-dev_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libgfortran-5-dev:armhf (5.2.1-23+rpi1+b1) ...
Selecting previously unselected package gfortran-5.
Preparing to unpack .../gfortran-5_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking gfortran-5 (5.2.1-23+rpi1+b1) ...
Selecting previously unselected package gfortran.
Preparing to unpack .../gfortran_4%3a5.2.1-4+rpi3_armhf.deb ...
Unpacking gfortran (4:5.2.1-4+rpi3) ...
Selecting previously unselected package libblas-common.
Preparing to unpack .../libblas-common_1.2.20110419-11_armhf.deb ...
Unpacking libblas-common (1.2.20110419-11) ...
Selecting previously unselected package libblas3.
Preparing to unpack .../libblas3_1.2.20110419-11_armhf.deb ...
Unpacking libblas3 (1.2.20110419-11) ...
Selecting previously unselected package libpixman-1-0:armhf.
Preparing to unpack .../libpixman-1-0_0.33.4-1_armhf.deb ...
Unpacking libpixman-1-0:armhf (0.33.4-1) ...
Selecting previously unselected package libxcb-render0:armhf.
Preparing to unpack .../libxcb-render0_1.10-3+b1_armhf.deb ...
Unpacking libxcb-render0:armhf (1.10-3+b1) ...
Selecting previously unselected package libxcb-shm0:armhf.
Preparing to unpack .../libxcb-shm0_1.10-3+b1_armhf.deb ...
Unpacking libxcb-shm0:armhf (1.10-3+b1) ...
Selecting previously unselected package libxrender1:armhf.
Preparing to unpack .../libxrender1_1%3a0.9.9-2_armhf.deb ...
Unpacking libxrender1:armhf (1:0.9.9-2) ...
Selecting previously unselected package libcairo2:armhf.
Preparing to unpack .../libcairo2_1.14.4-1_armhf.deb ...
Unpacking libcairo2:armhf (1.14.4-1) ...
Selecting previously unselected package libexpat1-dev:armhf.
Preparing to unpack .../libexpat1-dev_2.1.0-7_armhf.deb ...
Unpacking libexpat1-dev:armhf (2.1.0-7) ...
Selecting previously unselected package liblapack3.
Preparing to unpack .../liblapack3_3.5.0-5_armhf.deb ...
Unpacking liblapack3 (3.5.0-5) ...
Selecting previously unselected package libopenbabel4v5.
Preparing to unpack .../libopenbabel4v5_2.3.2+dfsg-2.2_armhf.deb ...
Unpacking libopenbabel4v5 (2.3.2+dfsg-2.2) ...
Selecting previously unselected package libpython2.7-dev:armhf.
Preparing to unpack .../libpython2.7-dev_2.7.10-5+b1_armhf.deb ...
Unpacking libpython2.7-dev:armhf (2.7.10-5+b1) ...
Selecting previously unselected package libpython-dev:armhf.
Preparing to unpack .../libpython-dev_2.7.9-1_armhf.deb ...
Unpacking libpython-dev:armhf (2.7.9-1) ...
Selecting previously unselected package libxml2-utils.
Preparing to unpack .../libxml2-utils_2.9.2+zdfsg1-4_armhf.deb ...
Unpacking libxml2-utils (2.9.2+zdfsg1-4) ...
Selecting previously unselected package libxslt1.1:armhf.
Preparing to unpack .../libxslt1.1_1.1.28-2.1_armhf.deb ...
Unpacking libxslt1.1:armhf (1.1.28-2.1) ...
Selecting previously unselected package openbabel.
Preparing to unpack .../openbabel_2.3.2+dfsg-2.2_armhf.deb ...
Unpacking openbabel (2.3.2+dfsg-2.2) ...
Selecting previously unselected package python2.7-dev.
Preparing to unpack .../python2.7-dev_2.7.10-5+b1_armhf.deb ...
Unpacking python2.7-dev (2.7.10-5+b1) ...
Selecting previously unselected package python-dev.
Preparing to unpack .../python-dev_2.7.9-1_armhf.deb ...
Unpacking python-dev (2.7.9-1) ...
Selecting previously unselected package python-numpy.
Preparing to unpack .../python-numpy_1%3a1.9.2-5_armhf.deb ...
Unpacking python-numpy (1:1.9.2-5) ...
Selecting previously unselected package scons.
Preparing to unpack .../archives/scons_2.4.1-1_all.deb ...
Unpacking scons (2.4.1-1) ...
Selecting previously unselected package swig3.0.
Preparing to unpack .../swig3.0_3.0.7-2_armhf.deb ...
Unpacking swig3.0 (3.0.7-2) ...
Selecting previously unselected package swig.
Preparing to unpack .../swig_3.0.7-2_armhf.deb ...
Unpacking swig (3.0.7-2) ...
Selecting previously unselected package xsltproc.
Preparing to unpack .../xsltproc_1.1.28-2.1_armhf.deb ...
Unpacking xsltproc (1.1.28-2.1) ...
Selecting previously unselected package xmlto.
Preparing to unpack .../xmlto_0.0.28-0.1_armhf.deb ...
Unpacking xmlto (0.0.28-0.1) ...
Selecting previously unselected package sbuild-build-depends-pdb2pqr-dummy.
Preparing to unpack .../sbuild-build-depends-pdb2pqr-dummy.deb ...
Unpacking sbuild-build-depends-pdb2pqr-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-22) ...
Setting up libgomp1:armhf (5.2.1-23+rpi1+b1) ...
Setting up libatomic1:armhf (5.2.1-23+rpi1+b1) ...
Setting up libasan2:armhf (5.2.1-23+rpi1+b1) ...
Setting up libubsan0:armhf (5.2.1-23+rpi1+b1) ...
Setting up libisl15:armhf (0.15-3) ...
Setting up cpp-5 (5.2.1-23+rpi1+b1) ...
Setting up libcc1-0:armhf (5.2.1-23+rpi1+b1) ...
Setting up libgcc-5-dev:armhf (5.2.1-23+rpi1+b1) ...
Setting up gcc-5 (5.2.1-23+rpi1+b1) ...
Setting up libstdc++-5-dev:armhf (5.2.1-23+rpi1+b1) ...
Setting up g++-5 (5.2.1-23+rpi1+b1) ...
Setting up groff-base (1.22.3-4) ...
Setting up bsdmainutils (9.0.6) ...
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 libpipeline1:armhf (1.4.1-1) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up mime-support (3.59) ...
Setting up libexpat1:armhf (2.1.0-7) ...
Setting up libffi6:armhf (3.2.1-3) ...
Setting up libsqlite3-0:armhf (3.9.2-1) ...
Setting up libssl1.0.2:armhf (1.0.2d-3) ...
Setting up libpython2.7-stdlib:armhf (2.7.10-5+b1) ...
Setting up python2.7 (2.7.10-5+b1) ...
Setting up libpython-stdlib:armhf (2.7.9-1) ...
Setting up python (2.7.9-1) ...
Setting up libfreetype6:armhf (2.6.1-0.1) ...
Setting up ucf (3.0031) ...
Setting up fonts-dejavu-core (2.35-1) ...
Setting up fontconfig-config (2.11.0-6.3) ...
Setting up libfontconfig1:armhf (2.11.0-6.3) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libxau6:armhf (1:1.0.8-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-1) ...
Setting up libxcb1:armhf (1.10-3+b1) ...
Setting up libx11-data (2:1.6.3-1) ...
Setting up libx11-6:armhf (2:1.6.3-1) ...
Setting up libxext6:armhf (2:1.3.3-1) ...
Setting up sgml-base (1.26+nmu4) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
Setting up libpython2.7:armhf (2.7.10-5+b1) ...
Setting up libicu55:armhf (55.1-6) ...
Setting up libxml2:armhf (2.9.2+zdfsg1-4) ...
Setting up cpp (4:5.2.1-4+rpi3) ...
Setting up libglib2.0-0:armhf (2.46.2-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.9-1) ...
Setting up gettext (0.19.6-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.18) ...
Setting up libarchive-zip-perl (1.53-1) ...
Setting up libfile-stripnondeterminism-perl (0.014-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up xml-core (0.13+nmu2) ...
Setting up gcc (4:5.2.1-4+rpi3) ...
Setting up libgfortran3:armhf (5.2.1-23+rpi1+b1) ...
Setting up libgfortran-5-dev:armhf (5.2.1-23+rpi1+b1) ...
Setting up gfortran-5 (5.2.1-23+rpi1+b1) ...
Setting up gfortran (4:5.2.1-4+rpi3) ...
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 libblas-common (1.2.20110419-11) ...
Setting up libblas3 (1.2.20110419-11) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libpixman-1-0:armhf (0.33.4-1) ...
Setting up libxcb-render0:armhf (1.10-3+b1) ...
Setting up libxcb-shm0:armhf (1.10-3+b1) ...
Setting up libxrender1:armhf (1:0.9.9-2) ...
Setting up libcairo2:armhf (1.14.4-1) ...
Setting up libexpat1-dev:armhf (2.1.0-7) ...
Setting up liblapack3 (3.5.0-5) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up libopenbabel4v5 (2.3.2+dfsg-2.2) ...
Setting up libpython2.7-dev:armhf (2.7.10-5+b1) ...
Setting up libpython-dev:armhf (2.7.9-1) ...
Setting up libxml2-utils (2.9.2+zdfsg1-4) ...
Setting up libxslt1.1:armhf (1.1.28-2.1) ...
Setting up openbabel (2.3.2+dfsg-2.2) ...
Setting up python2.7-dev (2.7.10-5+b1) ...
Setting up python-dev (2.7.9-1) ...
Setting up python-numpy (1:1.9.2-5) ...
Setting up scons (2.4.1-1) ...
Setting up swig3.0 (3.0.7-2) ...
Setting up swig (3.0.7-2) ...
Setting up xsltproc (1.1.28-2.1) ...
Processing triggers for sgml-base (1.26+nmu4) ...
Setting up sgml-data (2.0.10) ...
Setting up docbook-xsl (1.78.1+dfsg-1) ...
Processing triggers for sgml-base (1.26+nmu4) ...
Setting up docbook-xml (4.5-7.3) ...
Processing triggers for sgml-base (1.26+nmu4) ...
Setting up xmlto (0.0.28-0.1) ...
Setting up debhelper (9.20151005) ...
Setting up sbuild-build-depends-pdb2pqr-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.014-1) ...
Processing triggers for libc-bin (2.19-22) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.1-7 dpkg-dev_1.18.3 g++-5_5.2.1-23+rpi1+b1 gcc-5_5.2.1-23+rpi1+b1 libc6-dev_2.19-22 libstdc++-5-dev_5.2.1-23+rpi1+b1 libstdc++6_5.2.1-23+rpi1+b1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4+rpi1 base-passwd_3.5.38 bash_4.3-14 binutils_2.25.1-7 bsdmainutils_9.0.6 bsdutils_1:2.27.1-1 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.2.1-4+rpi3 cpp-5_5.2.1-23+rpi1+b1 dash_0.5.7-4 debconf_1.5.58 debconf-i18n_1.5.58 debfoster_2.7-2 debhelper_9.20151005 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-1+rpi1 docbook-xml_4.5-7.3 docbook-xsl_1.78.1+dfsg-1 dpkg_1.18.3 dpkg-dev_1.18.3 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.4.2-10 fontconfig-config_2.11.0-6.3 fonts-dejavu-core_2.35-1 g++_4:5.2.1-4+rpi2 g++-5_5.2.1-23+rpi1+b1 gcc_4:5.2.1-4+rpi3 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-1 gcc-4.9-base_4.9.3-5 gcc-5_5.2.1-23+rpi1+b1 gcc-5-base_5.2.1-23+rpi1+b1 gettext_0.19.6-1 gettext-base_0.19.6-1 gfortran_4:5.2.1-4+rpi3 gfortran-5_5.2.1-23+rpi1+b1 gnupg_1.4.19-6 gpgv_1.4.19-6 grep_2.22-1 groff-base_1.22.3-4 gzip_1.6-4 hostname_3.16 init_1.24 init-system-helpers_1.24 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-2+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.10-2+b2 libapt-pkg4.16_1.0.10.2 libarchive-zip-perl_1.53-1 libasan2_5.2.1-23+rpi1+b1 libatomic1_5.2.1-23+rpi1+b1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4 libaudit1_1:2.4.4-4 libblas-common_1.2.20110419-11 libblas3_1.2.20110419-11 libblkid1_2.27.1-1 libbz2-1.0_1.0.6-8 libc-bin_2.19-22 libc-dev-bin_2.19-22 libc6_2.19-22 libc6-dev_2.19-22 libcairo2_1.14.4-1 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.2.1-23+rpi1+b1 libcomerr2_1.42.13-1 libcroco3_0.6.9-1 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-11 libdbus-1-3_1.10.4-1 libdebconfclient0_0.197 libdevmapper1.02.1_2:1.02.110-1+rpi1 libdpkg-perl_1.18.3 libdrm2_2.4.65-3 libexpat1_2.1.0-7 libexpat1-dev_2.1.0-7 libfakeroot_1.20.2-1 libfdisk1_2.27.1-1 libffi6_3.2.1-3 libfile-stripnondeterminism-perl_0.014-1 libfontconfig1_2.11.0-6.3 libfreetype6_2.6.1-0.1 libgc1c2_1:7.4.2-7 libgcc-5-dev_5.2.1-23+rpi1+b1 libgcc1_1:5.2.1-23+rpi1+b1 libgcrypt20_1.6.4-3 libgdbm3_1.8.3-13.1 libgfortran-5-dev_5.2.1-23+rpi1+b1 libgfortran3_5.2.1-23+rpi1+b1 libglib2.0-0_2.46.2-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.2.1-23+rpi1+b1 libgpg-error0_1.20-1 libicu55_55.1-6 libisl13_0.14-2 libisl15_0.15-3 libklibc_2.0.4-2+rpi1 libkmod2_21-1 liblapack3_3.5.0-5 liblocale-gettext-perl_1.07-1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-1 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_6.0+20151024-2 libncursesw5_6.0+20151024-2 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libopenbabel4v5_2.3.2+dfsg-2.2 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-7.4 libpipeline1_1.4.1-1 libpixman-1-0_0.33.4-1 libpng12-0_1.2.54-1 libprocps4_2:3.3.10-2 libpython-dev_2.7.9-1 libpython-stdlib_2.7.9-1 libpython2.7_2.7.10-5+b1 libpython2.7-dev_2.7.10-5+b1 libpython2.7-minimal_2.7.10-5+b1 libpython2.7-stdlib_2.7.10-5+b1 libreadline6_6.3-8+b3 libseccomp2_2.2.3-2 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsmartcols1_2.27.1-1 libsqlite3-0_3.9.2-1 libss2_1.42.13-1 libssl1.0.2_1.0.2d-3 libstdc++-5-dev_5.2.1-23+rpi1+b1 libstdc++6_5.2.1-23+rpi1+b1 libsystemd0_228-2 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2 libubsan0_5.2.1-23+rpi1+b1 libudev1_228-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libxau6_1:1.0.8-1 libxcb-render0_1.10-3+b1 libxcb-shm0_1.10-3+b1 libxcb1_1.10-3+b1 libxdmcp6_1:1.1.2-1 libxext6_2:1.3.3-1 libxml2_2.9.2+zdfsg1-4 libxml2-utils_2.9.2+zdfsg1-4 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_4.1+Debian13+rpi1+nmu1 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.5-1 mawk_1.3.3-17 mime-support_3.59 mount_2.27.1-1 multiarch-support_2.19-22 nano_2.4.2-1 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 openbabel_2.3.2+dfsg-2.2 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 po-debconf_1.0.18 procps_2:3.3.10-2 python_2.7.9-1 python-dev_2.7.9-1 python-minimal_2.7.9-1 python-numpy_1:1.9.2-5 python2.7_2.7.10-5+b1 python2.7-dev_2.7.10-5+b1 python2.7-minimal_2.7.10-5+b1 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_2.4.1-1 sed_4.2.2-6.1 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_228-2 systemd-sysv_228-2 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-2.1 tzdata_2015g-1 ucf_3.0031 udev_228-2 util-linux_2.27.1-1 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 Thu Nov 26 19:25:51 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./pdb2pqr_2.0.0+dfsg-2.dsc
dpkg-source: info: extracting pdb2pqr in pdb2pqr-2.0.0+dfsg
dpkg-source: info: unpacking pdb2pqr_2.0.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking pdb2pqr_2.0.0+dfsg-2.debian.tar.xz
dpkg-source: info: applying fix-hashbangs.patch
dpkg-source: info: applying no_privacy_breach_logo.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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-5b5ee240-cab2-4269-918a-97fe12ac50f4
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package pdb2pqr
dpkg-buildpackage: source version 2.0.0+dfsg-2
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build pdb2pqr-2.0.0+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-2.0.0+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-2.0.0+dfsg'
dh_clean
debian/rules build-arch
dh build-arch --with python2
dh_testdir -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/«BUILDDIR»/pdb2pqr-2.0.0+dfsg'
dh_auto_configure
python scons/scons.py \
URL="http://localhost/pdb2pqr/" \
PREFIX="/usr/share/pdb2pqr"
scons: Reading SConscript files ...
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:1804:0,
from /usr/include/python2.7/numpy/ndarrayobject.h:17,
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: 2.0.0
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 simple 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-2.0.0+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
debian/rules override_dh_auto_install-arch
make[1]: Entering directory '/«BUILDDIR»/pdb2pqr-2.0.0+dfsg'
dh_auto_install -a
for app in /usr/share/pdb2pqr/pdb2pqr.py /usr/share/pdb2pqr/src/psize.py; do \
sed -e "s,@SCRIPT@,${app}," debian/wrapper.sh \
>debian/pdb2pqr/usr/bin/$(basename ${app} .py) && \
chmod 0755 debian/pdb2pqr/usr/bin/$(basename ${app} .py); \
done
for app in /usr/share/pdb2pqr/propka30/propka.py; do \
sed -e "s,@SCRIPT@,${app}," debian/wrapper.sh \
>debian/pdb2pqr/usr/bin/$(basename ${app} .py) && \
chmod 0755 debian/pdb2pqr/usr/bin/$(basename ${app} .py); \
done
make[1]: Leaving directory '/«BUILDDIR»/pdb2pqr-2.0.0+dfsg'
dh_install -a
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/«BUILDDIR»/pdb2pqr-2.0.0+dfsg'
dh_installchangelogs ChangeLog.md
make[1]: Leaving directory '/«BUILDDIR»/pdb2pqr-2.0.0+dfsg'
debian/rules override_dh_installman-arch
make[1]: Entering directory '/«BUILDDIR»/pdb2pqr-2.0.0+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-2.0.0+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-2.0.0+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 0755 debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py
make[1]: Leaving directory '/«BUILDDIR»/pdb2pqr-2.0.0+dfsg'
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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
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
dh_installdeb -a
dh_gencontrol -a
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' in '../pdb2pqr_2.0.0+dfsg-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pdb2pqr_2.0.0+dfsg-2_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build pdb2pqr-2.0.0+dfsg
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20151202-0600
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
pdb2pqr_2.0.0+dfsg-2_armhf.changes:
───────────────────────────────────
Format: 1.8
Date: Thu, 26 Nov 2015 20:08:19 +0100
Source: pdb2pqr
Binary: pdb2pqr pdb2pqr-doc
Architecture: armhf
Version: 2.0.0+dfsg-2
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard 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
Closes: 806222
Changes:
pdb2pqr (2.0.0+dfsg-2) unstable; urgency=medium
.
* Enable building arch independent packages separately
Closes: #806222
* Remove obsolete debian/pycompat
Checksums-Sha1:
558d6c548ef971430c41afb3c22a3456ccdb504f 348458 pdb2pqr_2.0.0+dfsg-2_armhf.deb
Checksums-Sha256:
bcf3a78facb025bebc2d102a97f0b32bcd1350e9e53dfa31db022230ea6ace40 348458 pdb2pqr_2.0.0+dfsg-2_armhf.deb
Files:
f85d4555fcadb4b4e31000380de753bc 348458 science optional pdb2pqr_2.0.0+dfsg-2_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
pdb2pqr_2.0.0+dfsg-2_armhf.deb
──────────────────────────────
new debian package, version 2.0.
size 348458 bytes: control archive=4798 bytes.
1359 bytes, 28 lines control
9112 bytes, 125 lines md5sums
182 bytes, 9 lines * postinst #!/bin/sh
251 bytes, 14 lines * prerm #!/bin/sh
Package: pdb2pqr
Version: 2.0.0+dfsg-2
Architecture: armhf
Maintainer: Debian Med <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2649
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), 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.
drwxr-xr-x root/root 0 2015-12-02 06:00 ./
drwxr-xr-x root/root 0 2015-12-02 05:59 ./usr/
drwxr-xr-x root/root 0 2015-12-02 05:59 ./usr/bin/
-rwxr-xr-x root/root 124 2015-12-02 05:59 ./usr/bin/pdb2pqr
-rwxr-xr-x root/root 132 2015-12-02 05:59 ./usr/bin/propka
-rwxr-xr-x root/root 126 2015-12-02 05:59 ./usr/bin/psize
drwxr-xr-x root/root 0 2015-12-02 05:59 ./usr/lib/
drwxr-xr-x root/root 0 2015-12-02 05:59 ./usr/lib/pdb2pqr/
drwxr-xr-x root/root 0 2015-12-02 06:00 ./usr/lib/pdb2pqr/pdb2pka/
-rw-r--r-- root/root 515152 2015-12-02 06:00 ./usr/lib/pdb2pqr/pdb2pka/_pMC_mult.so
drwxr-xr-x root/root 0 2015-12-02 06:00 ./usr/lib/pdb2pqr/pdb2pka/substruct/
-rw-r--r-- root/root 12396 2015-12-02 06:00 ./usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.so
drwxr-xr-x root/root 0 2015-12-02 06:00 ./usr/share/
drwxr-xr-x root/root 0 2015-12-02 05:59 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-12-02 06:00 ./usr/share/doc/pdb2pqr/
-rw-r--r-- root/root 30 2014-12-02 00:12 ./usr/share/doc/pdb2pqr/AUTHORS
-rw-r--r-- root/root 172 2014-12-02 00:12 ./usr/share/doc/pdb2pqr/NEWS.gz
-rw-r--r-- root/root 489 2013-09-12 08:58 ./usr/share/doc/pdb2pqr/README.Debian
-rw-r--r-- root/root 572 2014-12-02 00:12 ./usr/share/doc/pdb2pqr/README.md
-rw-r--r-- root/root 1193 2015-11-26 19:19 ./usr/share/doc/pdb2pqr/changelog.Debian.gz
-rw-r--r-- root/root 1344 2014-12-23 17:52 ./usr/share/doc/pdb2pqr/changelog.gz
-rw-r--r-- root/root 5190 2015-05-18 07:46 ./usr/share/doc/pdb2pqr/copyright
drwxr-xr-x root/root 0 2015-12-02 05:59 ./usr/share/man/
drwxr-xr-x root/root 0 2015-12-02 06:00 ./usr/share/man/man1/
-rw-r--r-- root/root 2083 2015-12-02 05:59 ./usr/share/man/man1/pdb2pqr.1.gz
-rw-r--r-- root/root 1044 2015-12-02 06:00 ./usr/share/man/man1/propka.1.gz
-rw-r--r-- root/root 1252 2015-12-02 05:59 ./usr/share/man/man1/psize.1.gz
drwxr-xr-x root/root 0 2015-12-02 05:59 ./usr/share/pdb2pqr/
drwxr-xr-x root/root 0 2015-12-02 05:59 ./usr/share/pdb2pqr/dat/
-rw-r--r-- root/root 58175 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/AA.xml
-rw-r--r-- root/root 60679 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/AMBER.DAT
-rw-r--r-- root/root 2290 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/AMBER.names
-rw-r--r-- root/root 64231 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/CHARMM.DAT
-rw-r--r-- root/root 6846 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/CHARMM.names
-rw-r--r-- root/root 4484 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/HYDROGENS.xml
-rw-r--r-- root/root 33840 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/NA.xml
-rw-r--r-- root/root 24406 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/PARSE.DAT
-rw-r--r-- root/root 5692 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/PARSE.names
-rw-r--r-- root/root 14806 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/PATCHES.xml
-rw-r--r-- root/root 29525 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/PEOEPB.DAT
-rw-r--r-- root/root 1672 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/PEOEPB.names
-rw-r--r-- root/root 34200 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/SWANSON.DAT
-rw-r--r-- root/root 1185 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/SWANSON.names
-rw-r--r-- root/root 62119 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/TOPOLOGY.xml
-rw-r--r-- root/root 97563 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/TYL06.DAT
-rw-r--r-- root/root 1993 2014-12-02 00:12 ./usr/share/pdb2pqr/dat/TYL06.names
drwxr-xr-x root/root 0 2015-12-02 05:59 ./usr/share/pdb2pqr/extensions/
-rw-r--r-- root/root 206 2014-12-02 00:12 ./usr/share/pdb2pqr/extensions/README
-rw-r--r-- root/root 4628 2014-12-02 00:12 ./usr/share/pdb2pqr/extensions/__init__.py
-rw-r--r-- root/root 1941 2014-12-02 00:12 ./usr/share/pdb2pqr/extensions/chi.py
-rw-r--r-- root/root 2843 2014-12-02 00:12 ./usr/share/pdb2pqr/extensions/contact.py
-rw-r--r-- root/root 6986 2014-12-02 00:12 ./usr/share/pdb2pqr/extensions/hbond.py
-rw-r--r-- root/root 13567 2014-12-02 00:12 ./usr/share/pdb2pqr/extensions/newresinter.py
-rw-r--r-- root/root 3339 2014-12-02 00:12 ./usr/share/pdb2pqr/extensions/rama.py
-rw-r--r-- root/root 12525 2014-12-02 00:12 ./usr/share/pdb2pqr/extensions/resinter.py
-rw-r--r-- root/root 3055 2014-12-02 00:12 ./usr/share/pdb2pqr/extensions/salt.py
-rw-r--r-- root/root 944 2014-12-02 00:12 ./usr/share/pdb2pqr/extensions/summary.py
-rw-r--r-- root/root 3219 2014-12-02 00:12 ./usr/share/pdb2pqr/extensions/template
-rw-r--r-- root/root 34380 2014-12-18 00:18 ./usr/share/pdb2pqr/main.py
-rw-r--r-- root/root 27728 2014-12-02 19:57 ./usr/share/pdb2pqr/main_cgi.py
drwxr-xr-x root/root 0 2015-12-02 06:00 ./usr/share/pdb2pqr/pdb2pka/
-rw-r--r-- root/root 28386 2014-12-02 00:12 ./usr/share/pdb2pqr/pdb2pka/NEWligand_topology.py
-rw-r--r-- root/root 0 2014-12-02 00:12 ./usr/share/pdb2pqr/pdb2pka/__init__.py
lrwxrwxrwx root/root 0 2015-12-02 06:00 ./usr/share/pdb2pqr/pdb2pka/_pMC_mult.so -> ../../../lib/pdb2pqr/pdb2pka/_pMC_mult.so
-rw-r--r-- root/root 14813 2014-12-04 20:34 ./usr/share/pdb2pqr/pdb2pka/apbs.py
-rw-r--r-- root/root 3425 2014-12-02 00:12 ./usr/share/pdb2pqr/pdb2pka/charge_mon.py
-rw-r--r-- root/root 7906 2014-12-02 00:12 ./usr/share/pdb2pqr/pdb2pka/example.py
-rw-r--r-- root/root 11384 2015-12-02 05:58 ./usr/share/pdb2pqr/pdb2pka/inputgen_pKa.py
-rw-r--r-- root/root 28394 2014-12-02 00:12 ./usr/share/pdb2pqr/pdb2pka/ligand_topology.py
drwxr-xr-x root/root 0 2015-12-02 05:59 ./usr/share/pdb2pqr/pdb2pka/ligandclean/
-rw-r--r-- root/root 26 2014-12-02 00:12 ./usr/share/pdb2pqr/pdb2pka/ligandclean/__init__.py
-rw-r--r-- root/root 13593 2014-12-02 00:12 ./usr/share/pdb2pqr/pdb2pka/ligandclean/ligff.py
-rw-r--r-- root/root 1004 2014-12-02 00:12 ./usr/share/pdb2pqr/pdb2pka/ligandclean/lookuptable.py
-rw-r--r-- root/root 5376 2014-12-02 00:12 ./usr/share/pdb2pqr/pdb2pka/ligandclean/peoe_PDB2PQR.py
-rw-r--r-- root/root 3969 2014-12-02 00:12 ./usr/share/pdb2pqr/pdb2pka/ligandclean/templates.py
-rw-r--r-- root/root 4703 2014-12-02 00:12 ./usr/share/pdb2pqr/pdb2pka/ligandclean/trial_templates.py
-rw-r--r-- root/root 33626 2014-12-02 19:57 ./usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py
-rw-r--r-- root/root 4862 2014-12-02 00:12 ./usr/share/pdb2pqr/pdb2pka/pKa_base.py
-rw-r--r-- root/root 5498 2014-12-02 00:12 ./usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py
-rw-r--r-- root/root 14881 2015-12-02 05:59 ./usr/share/pdb2pqr/pdb2pka/pMC_mult.py
-rw-r--r-- root/root 4683 2014-12-02 19:57 ./usr/share/pdb2pqr/pdb2pka/pka_help.py
-rw-r--r-- root/root 23018 2014-12-02 19:57 ./usr/share/pdb2pqr/pdb2pka/pka_old.py
-rw-r--r-- root/root 108808 2014-12-04 19:44 ./usr/share/pdb2pqr/pdb2pka/pka_routines.py
-rw-r--r-- root/root 8043 2014-12-02 00:12 ./usr/share/pdb2pqr/pdb2pka/prepare_pKa_ligand.py
drwxr-xr-x root/root 0 2015-12-02 06:00 ./usr/share/pdb2pqr/pdb2pka/substruct/
lrwxrwxrwx root/root 0 2015-12-02 06:00 ./usr/share/pdb2pqr/pdb2pka/substruct/Algorithms.so -> ../../../../lib/pdb2pqr/pdb2pka/substruct/Algorithms.so
-rw-r--r-- root/root 7 2014-12-02 00:12 ./usr/share/pdb2pqr/pdb2pka/substruct/__init__.py
-rwxr-xr-x root/root 2856 2015-12-02 06:00 ./usr/share/pdb2pqr/pdb2pqr.py
drwxr-xr-x root/root 0 2015-12-02 05:59 ./usr/share/pdb2pqr/propka30/
drwxr-xr-x root/root 0 2015-12-02 05:58 ./usr/share/pdb2pqr/propka30/Source/
-rw-r--r-- root/root 2599 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/__init__.py
-rw-r--r-- root/root 20906 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/bonds.py
-rw-r--r-- root/root 19234 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/calculator.py
-rw-r--r-- root/root 14960 2014-12-02 19:57 ./usr/share/pdb2pqr/propka30/Source/chain.py
-rw-r--r-- root/root 12520 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/compare.py
-rw-r--r-- root/root 6385 2015-12-02 05:58 ./usr/share/pdb2pqr/propka30/Source/corresponding_atoms.py
-rw-r--r-- root/root 16432 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/coupled_residues.py
-rw-r--r-- root/root 6861 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/debug.py
-rw-r--r-- root/root 2787 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/determinant.py
-rw-r--r-- root/root 13965 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/determinants.py
-rw-r--r-- root/root 447 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/ions.list
-rw-r--r-- root/root 15365 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/iterative.py
-rw-r--r-- root/root 26523 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/lib.py
-rw-r--r-- root/root 17617 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/ligand.py
-rw-r--r-- root/root 53378 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/mutate.py
-rw-r--r-- root/root 18444 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/output.py
-rw-r--r-- root/root 55865 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/parameters.py
-rw-r--r-- root/root 16695 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/parameters_new.py
-rw-r--r-- root/root 16293 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/parameters_std.py
-rw-r--r-- root/root 19340 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/pdb.py
-rw-r--r-- root/root 35519 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/protein.py
-rw-r--r-- root/root 3405 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/protein_bonds.dat
-rw-r--r-- root/root 19561 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/protonate.py
-rw-r--r-- root/root 26525 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/protonator.py
-rw-r--r-- root/root 31222 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/residue.py
-rw-r--r-- root/root 13156 2015-12-02 05:58 ./usr/share/pdb2pqr/propka30/Source/rotate.py
-rw-r--r-- root/root 12117 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/vector_algebra.py
-rw-r--r-- root/root 59592 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/Source/version.py
-rw-r--r-- root/root 2404 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/__init__.py
-rw-r--r-- root/root 7215 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/compare.py
-rw-r--r-- root/root 12623 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/experiment.py
-rwxr-xr-x root/root 3039 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/propka.py
-rw-r--r-- root/root 3565 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/propka_det.py
-rw-r--r-- root/root 4015 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/propka_gui.py
-rw-r--r-- root/root 4095 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/propka_mut.py
-rw-r--r-- root/root 2978 2014-12-02 00:12 ./usr/share/pdb2pqr/propka30/propka_pdb.py
drwxr-xr-x root/root 0 2015-12-02 05:59 ./usr/share/pdb2pqr/src/
-rw-r--r-- root/root 0 2014-12-02 00:12 ./usr/share/pdb2pqr/src/__init__.py
-rw-r--r-- root/root 25195 2014-12-02 19:57 ./usr/share/pdb2pqr/src/aa.py
-rw-r--r-- root/root 3172 2015-12-02 05:59 ./usr/share/pdb2pqr/src/aconf.py
-rw-r--r-- root/root 3183 2014-12-02 00:12 ./usr/share/pdb2pqr/src/aconf.py.in
-rw-r--r-- root/root 13623 2014-12-02 00:12 ./usr/share/pdb2pqr/src/definitions.py
-rw-r--r-- root/root 3630 2014-12-02 19:57 ./usr/share/pdb2pqr/src/errors.py
-rw-r--r-- root/root 35074 2014-12-02 00:12 ./usr/share/pdb2pqr/src/forcefield.py
-rw-r--r-- root/root 104261 2014-12-02 19:57 ./usr/share/pdb2pqr/src/hydrogens.py
-rw-r--r-- root/root 17956 2014-12-02 00:12 ./usr/share/pdb2pqr/src/inputgen.py
-rw-r--r-- root/root 9417 2014-12-02 00:12 ./usr/share/pdb2pqr/src/na.py
-rw-r--r-- root/root 99727 2014-12-18 00:21 ./usr/share/pdb2pqr/src/pdb.py
-rw-r--r-- root/root 13242 2014-12-02 19:57 ./usr/share/pdb2pqr/src/protein.py
-rw-r--r-- root/root 18231 2014-12-02 19:57 ./usr/share/pdb2pqr/src/psize.py
-rw-r--r-- root/root 15573 2014-12-02 00:12 ./usr/share/pdb2pqr/src/quatfit.py
-rw-r--r-- root/root 69360 2014-12-02 19:57 ./usr/share/pdb2pqr/src/routines.py
-rw-r--r-- root/root 18562 2014-12-02 00:12 ./usr/share/pdb2pqr/src/server.py
-rw-r--r-- root/root 18515 2014-12-02 00:12 ./usr/share/pdb2pqr/src/server.py.in
-rw-r--r-- root/root 28614 2014-12-02 19:57 ./usr/share/pdb2pqr/src/structures.py
-rw-r--r-- root/root 14825 2014-12-02 00:12 ./usr/share/pdb2pqr/src/topology.py
-rw-r--r-- root/root 16711 2014-12-02 00:12 ./usr/share/pdb2pqr/src/utilities.py
drwxr-xr-x root/root 0 2015-12-02 06:00 ./usr/share/python/
drwxr-xr-x root/root 0 2015-12-02 06:00 ./usr/share/python/runtime.d/
-rwxr-xr-x root/root 136 2015-12-02 06:00 ./usr/share/python/runtime.d/pdb2pqr.rtupdate
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 31288
Build-Time: 104
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 611
Job: pdb2pqr_2.0.0+dfsg-2
Machine Architecture: armhf
Package: pdb2pqr
Package-Time: 775
Source-Version: 2.0.0+dfsg-2
Space: 31288
Status: successful
Version: 2.0.0+dfsg-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20151202-0600
Build needed 00:12:55, 31288k disc space