pdb2pqr →
1.9.0+dfsg-1 →
armhf → 2014-04-27 06:41:04
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ pdb2pqr 1.9.0+dfsg-1 (armhf) 27 Apr 2014 06:28 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: pdb2pqr
Version: 1.9.0+dfsg-1
Source Version: 1.9.0+dfsg-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/pdb2pqr-xvSGyv/pdb2pqr-1.9.0+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/pdb2pqr-xvSGyv' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-cfec5d08-5d38-4286-9bd5-1a8b89eff88c' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7385 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8555 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 16.0 MB in 37s (428 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 1518 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main pdb2pqr 1.9.0+dfsg-1 (dsc) [2145 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main pdb2pqr 1.9.0+dfsg-1 (tar) [1506 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main pdb2pqr 1.9.0+dfsg-1 (diff) [9852 B]
Fetched 1518 kB in 0s (4150 kB/s)
Download complete and in download only mode
Check arch
──────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-S4L5x4/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
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 47 not upgraded.
Need to get 0 B/816 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 ... 11599 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: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), gfortran, swig, xmlto, openbabel, python-dev, python-numpy, scons
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), gfortran, swig, xmlto, openbabel, python-dev, python-numpy, scons
dpkg-deb: building package `sbuild-build-depends-pdb2pqr-dummy' in `/«BUILDDIR»/resolver-qA6hH7/apt_archive/sbuild-build-depends-pdb2pqr-dummy.deb'.
OK
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 debhelper docbook-xml docbook-xsl file fontconfig-config
fonts-dejavu-core gcc gettext gettext-base gfortran gfortran-4.8 groff-base
intltool-debian libasprintf0c2 libblas3 libcairo2 libcroco3 libdrm2
libexpat1 libexpat1-dev libffi6 libfontconfig1 libfreetype6 libgcrypt11
libgfortran-4.8-dev libgfortran3 libgl1-mesa-glx libglapi-mesa libglib2.0-0
libgpg-error0 liblapack3 libmagic1 libopenbabel4 libpipeline1 libpixman-1-0
libpng12-0 libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev
libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libssl1.0.0
libunistring0 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0
libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0
libxcb-sync1 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxml2
libxml2-utils libxrender1 libxshmfence1 libxslt1.1 libxxf86vm1 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 swig2.0 ucf xml-core xmlto xsltproc
Suggested packages:
wamerican wordlist whois vacation cpp-doc 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-multilib manpages-dev autoconf
automake1.9 libtool flex bison gdb gcc-doc gettext-doc gfortran-doc
gfortran-4.8-doc libgfortran3-dbg groff rng-tools 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 swig2.0-examples swig2.0-doc xmltex
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libgl1-mesa-dri libglib2.0-data shared-mime-info libmail-sendmail-perl
libpaper-utils zip
The following NEW packages will be installed:
bsdmainutils debhelper docbook-xml docbook-xsl file fontconfig-config
fonts-dejavu-core gettext gettext-base gfortran gfortran-4.8 groff-base
intltool-debian libasprintf0c2 libblas3 libcairo2 libcroco3 libdrm2
libexpat1 libexpat1-dev libffi6 libfontconfig1 libfreetype6 libgcrypt11
libgfortran-4.8-dev libgfortran3 libgl1-mesa-glx libglapi-mesa libglib2.0-0
libgpg-error0 liblapack3 libmagic1 libopenbabel4 libpipeline1 libpixman-1-0
libpng12-0 libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev
libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libssl1.0.0
libunistring0 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0
libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0
libxcb-sync1 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxml2
libxml2-utils libxrender1 libxshmfence1 libxslt1.1 libxxf86vm1 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 swig2.0
ucf xml-core xmlto xsltproc
The following packages will be upgraded:
cpp gcc
2 upgraded, 88 newly installed, 0 to remove and 45 not upgraded.
Need to get 59.0 MB/59.0 MB of archives.
After this operation, 152 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.3.0-1 [21.1 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main libssl1.0.0 armhf 1.0.1g-3 [824 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-5 [962 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.7.1-1 [964 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.2-1 [29.0 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libgpg-error0 armhf 1.12-0.2 [78.9 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libgcrypt11 armhf 1.5.3-4 [233 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.17-1 [225 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libpython2.7-minimal armhf 2.7.6-8 [346 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main mime-support all 3.54 [36.4 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main libexpat1 armhf 2.1.0-4 [117 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.1~rc1+r3.0.13-12 [17.6 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main libsqlite3-0 armhf 3.8.4.3-1 [352 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main libpython2.7-stdlib armhf 2.7.6-8 [1827 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main libpython2.7 armhf 2.7.6-8 [883 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-3 [836 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main python2.7-minimal armhf 2.7.6-8 [1092 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main libpng12-0 armhf 1.2.50-1 [180 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main libfreetype6 armhf 2.5.2-1 [397 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main ucf all 3.0027+nmu1 [70.6 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main fonts-dejavu-core all 2.34-1 [1047 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main fontconfig-config all 2.11.0-5 [273 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main libfontconfig1 armhf 2.11.0-5 [310 kB]
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Get:27 http://172.17.0.1/private/ jessie-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:28 http://172.17.0.1/private/ jessie-staging/main libxdmcp6 armhf 1:1.1.1-1 [24.6 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main libxcb1 armhf 1.10-2 [36.9 kB]
Get:30 http://172.17.0.1/private/ jessie-staging/main libx11-data all 2:1.6.2-1 [125 kB]
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Get:32 http://172.17.0.1/private/ jessie-staging/main libx11-xcb1 armhf 2:1.6.2-1 [163 kB]
Get:33 http://172.17.0.1/private/ jessie-staging/main libxcb-dri2-0 armhf 1.10-2 [11.8 kB]
Get:34 http://172.17.0.1/private/ jessie-staging/main libxcb-dri3-0 armhf 1.10-2 [10.3 kB]
Get:35 http://172.17.0.1/private/ jessie-staging/main libxcb-glx0 armhf 1.10-2 [23.2 kB]
Get:36 http://172.17.0.1/private/ jessie-staging/main libxcb-present0 armhf 1.10-2 [10.4 kB]
Get:37 http://172.17.0.1/private/ jessie-staging/main libxcb-sync1 armhf 1.10-2 [12.9 kB]
Get:38 http://172.17.0.1/private/ jessie-staging/main libxfixes3 armhf 1:5.0.1-1 [21.0 kB]
Get:39 http://172.17.0.1/private/ jessie-staging/main libxdamage1 armhf 1:1.1.4-1 [14.6 kB]
Get:40 http://172.17.0.1/private/ jessie-staging/main libxext6 armhf 2:1.3.2-1 [51.1 kB]
Get:41 http://172.17.0.1/private/ jessie-staging/main libxshmfence1 armhf 1.1-2 [6736 B]
Get:42 http://172.17.0.1/private/ jessie-staging/main libxxf86vm1 armhf 1:1.1.3-1 [20.0 kB]
Get:43 http://172.17.0.1/private/ jessie-staging/main libgl1-mesa-glx armhf 10.1.0-5 [134 kB]
Get:44 http://172.17.0.1/private/ jessie-staging/main libpixman-1-0 armhf 0.32.4-1 [476 kB]
Get:45 http://172.17.0.1/private/ jessie-staging/main libxcb-render0 armhf 1.10-2 [15.7 kB]
Get:46 http://172.17.0.1/private/ jessie-staging/main libxcb-shm0 armhf 1.10-2 [10.8 kB]
Get:47 http://172.17.0.1/private/ jessie-staging/main libxrender1 armhf 1:0.9.8-1 [30.4 kB]
Get:48 http://172.17.0.1/private/ jessie-staging/main libcairo2 armhf 1.12.16-2+rpi1 [894 kB]
Get:49 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.40.0-2+rpi1 [2249 kB]
Get:50 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:51 http://172.17.0.1/private/ jessie-staging/main libgfortran3 armhf 4.8.2-16 [153 kB]
Get:52 http://172.17.0.1/private/ jessie-staging/main libexpat1-dev armhf 2.1.0-4 [210 kB]
Get:53 http://172.17.0.1/private/ jessie-staging/main libpython2.7-dev armhf 2.7.6-8 [21.6 MB]
Get:54 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:55 http://172.17.0.1/private/ jessie-staging/main libxslt1.1 armhf 1.1.28-2 [243 kB]
Get:56 http://172.17.0.1/private/ jessie-staging/main sgml-base all 1.26+nmu4 [14.6 kB]
Get:57 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.17-1 [55.3 kB]
Get:58 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3.2-1 [112 kB]
Get:59 http://172.17.0.1/private/ jessie-staging/main python2.7 armhf 2.7.6-8 [239 kB]
Get:60 http://172.17.0.1/private/ jessie-staging/main python-minimal armhf 2.7.5-5 [43.1 kB]
Get:61 http://172.17.0.1/private/ jessie-staging/main libpython-stdlib armhf 2.7.5-5 [19.8 kB]
Get:62 http://172.17.0.1/private/ jessie-staging/main python armhf 2.7.5-5 [180 kB]
Get:63 http://172.17.0.1/private/ jessie-staging/main cpp armhf 4:4.8.2-3 [16.6 kB]
Get:64 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3.2-1 [1137 kB]
Get:65 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:66 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:67 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20140228 [691 kB]
Get:68 http://172.17.0.1/private/ jessie-staging/main xml-core all 0.13+nmu2 [24.2 kB]
Get:69 http://172.17.0.1/private/ jessie-staging/main sgml-data all 2.0.9-1 [281 kB]
Get:70 http://172.17.0.1/private/ jessie-staging/main docbook-xml all 4.5-7.2 [347 kB]
Get:71 http://172.17.0.1/private/ jessie-staging/main docbook-xsl all 1.78.1+dfsg-1 [2339 kB]
Get:72 http://172.17.0.1/private/ jessie-staging/main gcc armhf 4:4.8.2-3 [5096 B]
Get:73 http://172.17.0.1/private/ jessie-staging/main libgfortran-4.8-dev armhf 4.8.2-16 [180 kB]
Get:74 http://172.17.0.1/private/ jessie-staging/main gfortran-4.8 armhf 4.8.2-16 [4094 kB]
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Get:76 http://172.17.0.1/private/ jessie-staging/main libblas3 armhf 1.2.20110419-7 [186 kB]
Get:77 http://172.17.0.1/private/ jessie-staging/main liblapack3 armhf 3.5.0-2 [2416 kB]
Get:78 http://172.17.0.1/private/ jessie-staging/main libopenbabel4 armhf 2.3.2+dfsg-1.1 [2485 kB]
Get:79 http://172.17.0.1/private/ jessie-staging/main libpython-dev armhf 2.7.5-5 [19.9 kB]
Get:80 http://172.17.0.1/private/ jessie-staging/main libxml2-utils armhf 2.9.1+dfsg1-3 [96.4 kB]
Get:81 http://172.17.0.1/private/ jessie-staging/main openbabel armhf 2.3.2+dfsg-1.1 [245 kB]
Get:82 http://172.17.0.1/private/ jessie-staging/main python2.7-dev armhf 2.7.6-8 [280 kB]
Get:83 http://172.17.0.1/private/ jessie-staging/main python-dev armhf 2.7.5-5 [1088 B]
Get:84 http://172.17.0.1/private/ jessie-staging/main python-numpy armhf 1:1.8.1-1 [1468 kB]
Get:85 http://172.17.0.1/private/ jessie-staging/main scons all 2.3.0-2 [609 kB]
Get:86 http://172.17.0.1/private/ jessie-staging/main swig2.0 armhf 2.0.11-1 [1387 kB]
Get:87 http://172.17.0.1/private/ jessie-staging/main swig armhf 2.0.11-1 [283 kB]
Get:88 http://172.17.0.1/private/ jessie-staging/main xsltproc armhf 1.1.28-2 [119 kB]
Get:89 http://172.17.0.1/private/ jessie-staging/main xmlto armhf 0.0.25-2 [36.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up gcc (4:4.8.2-3) ...
Setting up libgfortran-4.8-dev:armhf (4.8.2-16) ...
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update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
Setting up libblas3 (1.2.20110419-7) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
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update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.13-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24-3 dpkg-dev_1.17.6+rpi1 g++-4.8_4.8.2-16 gcc-4.8_4.8.2-16 libc6-dev_2.18-4 libstdc++-4.8-dev_4.8.2-16 libstdc++6_4.8.2-16 linux-libc-dev_3.12.6-2+rpi1
Package versions: apt_0.9.15.4 base-files_7.2+rpi1 base-passwd_3.5.28 bash_4.2+dfsg-1 binutils_2.24-3 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.6 build-essential_11.6 bzip2_1.0.6-5 coreutils_8.21-1 cpio_2.11+dfsg-1 cpp_4:4.8.2-3 cpp-4.8_4.8.2-16 dash_0.5.7-4 debconf_1.5.52 debconf-i18n_1.5.52 debfoster_2.7-1.2 debhelper_9.20140228 debianutils_4.4 diffutils_1:3.3-1 docbook-xml_4.5-7.2 docbook-xsl_1.78.1+dfsg-1 dpkg_1.17.6+rpi1 dpkg-dev_1.17.6+rpi1 e2fslibs_1.42.9-3 e2fsprogs_1.42.9-3 fakeroot_1.18.4-2 file_1:5.17-1 findutils_4.4.2-7 fontconfig-config_2.11.0-5 fonts-dejavu-core_2.34-1 g++_4:4.8.2-2 g++-4.8_4.8.2-16 gcc_4:4.8.2-3 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-10+rpi1 gcc-4.8_4.8.2-16 gcc-4.8-base_4.8.2-16 gettext_0.18.3.2-1 gettext-base_0.18.3.2-1 gfortran_4:4.8.2-3 gfortran-4.8_4.8.2-16 gnupg_1.4.16-1.1 gpgv_1.4.16-1.1 grep_2.16-1 groff-base_1.22.2-5 gzip_1.6-3 hostname_3.15 initramfs-tools_0.115 initscripts_2.88dsf-51 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.2-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_0.9.15.4 libasan0_4.8.2-16 libasprintf0c2_0.18.3.2-1 libatomic1_4.8.2-16 libattr1_1:2.4.47-1 libaudit-common_1:2.3.3-4 libaudit1_1:2.3.3-4 libblas3_1.2.20110419-7 libblkid1_2.20.1-5.6 libbz2-1.0_1.0.6-5 libc-bin_2.18-4 libc-dev-bin_2.18-4 libc6_2.18-4 libc6-dev_2.18-4 libcairo2_1.12.16-2+rpi1 libcap2_1:2.22-1.2 libcloog-isl4_0.18.2-1 libcomerr2_1.42.9-3 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdb5.3_5.3.28-3 libdbus-1-3_1.8.0-1 libdpkg-perl_1.17.6+rpi1 libdrm2_2.4.52-1 libexpat1_2.1.0-4 libexpat1-dev_2.1.0-4 libffi6_3.1~rc1+r3.0.13-12 libfontconfig1_2.11.0-5 libfreetype6_2.5.2-1 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.2-16 libgcc1_1:4.8.2-16 libgcrypt11_1.5.3-4 libgdbm3_1.8.3-12 libgfortran-4.8-dev_4.8.2-16 libgfortran3_4.8.2-16 libgl1-mesa-glx_10.1.0-5 libglapi-mesa_10.1.0-5 libglib2.0-0_2.40.0-2+rpi1 libgmp10_2:5.1.3+dfsg-1 libgomp1_4.8.2-16 libgpg-error0_1.12-0.2 libisl10_0.12.2-1 libklibc_2.0.2-1+rpi1 libkmod2_16-2 liblapack3_3.5.0-2 liblocale-gettext-perl_1.05-7+b3 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.17-1 libmount1_2.20.1-5.6 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncursesw5_5.9+20140118-1 libopenbabel4_2.3.2+dfsg-1.1 libpam-modules_1.1.8-2 libpam-modules-bin_1.1.8-2 libpam-runtime_1.1.8-2 libpam0g_1.1.8-2 libpcre3_1:8.31-2 libpipeline1_1.3.0-1 libpixman-1-0_0.32.4-1 libpng12-0_1.2.50-1 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-2 libpython-dev_2.7.5-5 libpython-stdlib_2.7.5-5 libpython2.7_2.7.6-8 libpython2.7-dev_2.7.6-8 libpython2.7-minimal_2.7.6-8 libpython2.7-stdlib_2.7.6-8 libreadline6_6.2+dfsg-0.1 libselinux1_2.2.2-1 libsemanage-common_2.2-1 libsemanage1_2.2-1 libsepol1_2.2-1 libslang2_2.2.4-16 libsqlite3-0_3.8.4.3-1 libss2_1.42.9-3 libssl1.0.0_1.0.1g-3 libstdc++-4.8-dev_4.8.2-16 libstdc++6_4.8.2-16 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-1 libtinfo5_5.9+20140118-1 libudev1_204-7 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.6 libx11-6_2:1.6.2-1 libx11-data_2:1.6.2-1 libx11-xcb1_2:1.6.2-1 libxau6_1:1.0.8-1 libxcb-dri2-0_1.10-2 libxcb-dri3-0_1.10-2 libxcb-glx0_1.10-2 libxcb-present0_1.10-2 libxcb-render0_1.10-2 libxcb-shm0_1.10-2 libxcb-sync1_1.10-2 libxcb1_1.10-2 libxdamage1_1:1.1.4-1 libxdmcp6_1:1.1.1-1 libxext6_2:1.3.2-1 libxfixes3_1:5.0.1-1 libxml2_2.9.1+dfsg1-3 libxml2-utils_2.9.1+dfsg1-3 libxrender1_1:0.9.8-1 libxshmfence1_1.1-2 libxslt1.1_1.1.28-2 libxxf86vm1_1:1.1.3-1 linux-libc-dev_3.12.6-2+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian12+rpi1 make_3.81-8.3 makedev_2.3.1-93 man-db_2.6.7.1-1 mawk_1.3.3-17 mime-support_3.54 mount_2.20.1-5.6 multiarch-support_2.18-4 nano_2.2.6-1 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 openbabel_2.3.2+dfsg-1.1 passwd_1:4.1.5.1-1 patch_2.7.1-4 perl_5.18.2-2 perl-base_5.18.2-2 perl-modules_5.18.2-2 plymouth_0.8.8-6+deb8u3 po-debconf_1.0.16+nmu2 procps_1:3.3.9-2 python_2.7.5-5 python-dev_2.7.5-5 python-minimal_2.7.5-5 python-numpy_1:1.8.1-1 python2.7_2.7.6-8 python2.7-dev_2.7.6-8 python2.7-minimal_2.7.6-8 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pdb2pqr-dummy_0.invalid.0 scons_2.3.0-2 sed_4.2.2-4 sensible-utils_0.0.9 sgml-base_1.26+nmu4 sgml-data_2.0.9-1 swig_2.0.11-1 swig2.0_2.0.11-1 sysv-rc_2.88dsf-51 sysvinit_2.88dsf-51 sysvinit-core_2.88dsf-51 sysvinit-utils_2.88dsf-51 tar_1.27.1-1 tzdata_2013i-1 ucf_3.0027+nmu1 udev_204-7 util-linux_2.20.1-5.6 xml-core_0.13+nmu2 xmlto_0.0.25-2 xsltproc_1.1.28-2 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon Apr 21 16:57:08 2014 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./pdb2pqr_1.9.0+dfsg-1.dsc
dpkg-source: info: extracting pdb2pqr in pdb2pqr-1.9.0+dfsg
dpkg-source: info: unpacking pdb2pqr_1.9.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking pdb2pqr_1.9.0+dfsg-1.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
────────────────
APT_CONFIG=/var/lib/sbuild/apt.conf
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-cfec5d08-5d38-4286-9bd5-1a8b89eff88c
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
init=/sbin/init
previous=N
rootmnt=/root
runlevel=2
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package pdb2pqr
dpkg-buildpackage: source version 1.9.0+dfsg-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build pdb2pqr-1.9.0+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-1.9.0+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-1.9.0+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-1.9.0+dfsg'
dh_auto_configure
python scons/scons.py
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/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 pdb2pka/pMC_mult.os pdb2pka/pMC_mult_wrap.os -L/usr/lib -lpython2.7
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:1761:0,
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 pdb2pka/substruct/Algorithms.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/_pMC_mult.so', 'pdb2pka/substruct/Algorithms.so']
========================
Configuration Parameters
========================
Version: 1.9.0
Install directory: /sbuild-nonexistent/pdb2pqr/
pdb2pka and ligand support: True
Path to the website directory: http://bm-wb-02/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 /sbuild-nonexistent/pdb2pqr/
Run "python scons/scons.py test", "scons/scons.py advtest", or "scons/scons.py complete-test" to run various pdb2pqr tests.
To setup a web service create a symbolic link to /sbuild-nonexistent/pdb2pqr/ that enables you to view http://bm-wb-02/pdb2pqr/ after running "scons/scons.py install"
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-1.9.0+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
make[1]: Entering directory `/«BUILDDIR»/pdb2pqr-1.9.0+dfsg'
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
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-1.9.0+dfsg'
dh_install -a
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory `/«BUILDDIR»/pdb2pqr-1.9.0+dfsg'
dh_installchangelogs ChangeLog.md
make[1]: Leaving directory `/«BUILDDIR»/pdb2pqr-1.9.0+dfsg'
dh_installman -a
dh_python2 -a
dh_perl -a
dh_link -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory `/«BUILDDIR»/pdb2pqr-1.9.0+dfsg'
dh_fixperms
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-1.9.0+dfsg'
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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_1.9.0+dfsg-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pdb2pqr_1.9.0+dfsg-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build pdb2pqr-1.9.0+dfsg
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140427-0639
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
pdb2pqr_1.9.0+dfsg-1_armhf.changes:
───────────────────────────────────
Format: 1.8
Date: Sat, 19 Apr 2014 15:49:25 +0200
Source: pdb2pqr
Binary: pdb2pqr pdb2pqr-doc
Architecture: armhf
Version: 1.9.0+dfsg-1
Distribution: jessie-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
Changes:
pdb2pqr (1.9.0+dfsg-1) unstable; urgency=medium
.
* New upstream version
* Adapted watch file
* Move debian/upstream to debian/upstream/metadata
* cme fix dpkg-control
* debian/patches/no_privacy_breach_logo.patch: remove potential
privacy breach logo
* drop autotools from Build-Depends since build system was changed
Checksums-Sha1:
c0de589a40c0380ac99dc81a29eb3cc240decc0c 350920 pdb2pqr_1.9.0+dfsg-1_armhf.deb
Checksums-Sha256:
70a539569a75aa7adbcdf4c7395c610c76da550ac5ddb18620bb69c7cd639e3b 350920 pdb2pqr_1.9.0+dfsg-1_armhf.deb
Files:
4243a26650c69fa12ccb91b3e5e48d36 350920 science optional pdb2pqr_1.9.0+dfsg-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
pdb2pqr_1.9.0+dfsg-1_armhf.deb
──────────────────────────────
new debian package, version 2.0.
size 350920 bytes: control archive=5172 bytes.
1361 bytes, 28 lines control
9108 bytes, 125 lines md5sums
182 bytes, 9 lines * postinst #!/bin/sh
251 bytes, 14 lines * prerm #!/bin/sh
Package: pdb2pqr
Version: 1.9.0+dfsg-1
Architecture: armhf
Maintainer: Debian Med <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2578
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libpython2.7 (>= 2.7), libstdc++6 (>= 4.4.0), 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 2014-04-27 06:39 ./
drwxr-xr-x root/root 0 2014-04-27 06:39 ./usr/
drwxr-xr-x root/root 0 2014-04-27 06:39 ./usr/bin/
-rwxr-xr-x root/root 124 2014-04-27 06:39 ./usr/bin/pdb2pqr
-rwxr-xr-x root/root 126 2014-04-27 06:39 ./usr/bin/psize
-rwxr-xr-x root/root 132 2014-04-27 06:39 ./usr/bin/propka
drwxr-xr-x root/root 0 2014-04-27 06:39 ./usr/lib/
drwxr-xr-x root/root 0 2014-04-27 06:39 ./usr/lib/pdb2pqr/
drwxr-xr-x root/root 0 2014-04-27 06:39 ./usr/lib/pdb2pqr/pdb2pka/
drwxr-xr-x root/root 0 2014-04-27 06:39 ./usr/lib/pdb2pqr/pdb2pka/substruct/
-rw-r--r-- root/root 12752 2014-04-27 06:39 ./usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.so
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
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Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 29656
Build-Time: 111
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 500
Job: pdb2pqr_1.9.0+dfsg-1
Machine Architecture: armhf
Package: pdb2pqr
Package-Time: 670
Source-Version: 1.9.0+dfsg-1
Space: 29656
Status: successful
Version: 1.9.0+dfsg-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140427-0639
Build needed 00:11:10, 29656k disc space