pdb2pqr →
2.0.0+dfsg-1 →
armhf → 2015-05-24 05:25:30
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-04
╔══════════════════════════════════════════════════════════════════════════════╗
║ pdb2pqr 2.0.0+dfsg-1 (armhf) 24 May 2015 05:12 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: pdb2pqr
Version: 2.0.0+dfsg-1
Source Version: 2.0.0+dfsg-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/pdb2pqr-EeUkzB/pdb2pqr-2.0.0+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/pdb2pqr-EeUkzB' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-95101614-b546-4341-9992-6015ca6e8a2b' 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 [7897 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [9672 kB]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
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Check APT
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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-1 (dsc) [2159 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main pdb2pqr 2.0.0+dfsg-1 (tar) [1784 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main pdb2pqr 2.0.0+dfsg-1 (diff) [9896 B]
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-ZaDpk5/apt_archive/sbuild-build-depends-core-dummy.deb'.
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
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Installing build dependencies
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Building dependency tree...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
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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-TJeIwJ/apt_archive/sbuild-build-depends-pdb2pqr-dummy.deb'.
OK
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┌──────────────────────────────────────────────────────────────────────────────┐
│ 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-4.9 debhelper docbook-xml docbook-xsl file
fontconfig-config fonts-dejavu-core g++-4.9 gcc gcc-4.9 gcc-4.9-base
gcc-5-base gettext gettext-base gfortran gfortran-4.9 groff-base
intltool-debian libasan1 libasprintf0c2 libatomic1 libblas-common libblas3
libcairo2 libcroco3 libexpat1 libexpat1-dev libffi6 libfontconfig1
libfreetype6 libgcc-4.9-dev libgcc1 libgfortran-4.9-dev libgfortran3
libglib2.0-0 libgomp1 libisl13 liblapack3 libmagic1 libopenbabel4
libpipeline1 libpixman-1-0 libpython-dev libpython-stdlib libpython2.7
libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libsqlite3-0
libssl1.0.0 libstdc++-4.9-dev libstdc++6 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 swig2.0 ucf
xml-core xmlto xsltproc
Suggested packages:
wamerican wordlist whois vacation cpp-doc gcc-4.9-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-4.9-doc
libstdc++6-4.9-dbg gcc-multilib manpages-dev autoconf automake libtool flex
bison gdb gcc-doc libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
libasan1-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg
libquadmath-dbg gettext-doc gfortran-doc gfortran-4.9-doc libgfortran3-dbg
groff libstdc++-4.9-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
swig2.0-examples swig2.0-doc xmltex
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xdg-user-dirs 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 gcc-5-base gettext gettext-base gfortran gfortran-4.9
groff-base intltool-debian libasprintf0c2 libblas-common libblas3 libcairo2
libcroco3 libexpat1 libexpat1-dev libffi6 libfontconfig1 libfreetype6
libgfortran-4.9-dev libgfortran3 libglib2.0-0 libisl13 liblapack3 libmagic1
libopenbabel4 libpipeline1 libpixman-1-0 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 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 swig2.0 ucf xml-core xmlto xsltproc
The following packages will be upgraded:
cpp cpp-4.9 g++-4.9 gcc gcc-4.9 gcc-4.9-base libasan1 libatomic1
libgcc-4.9-dev libgcc1 libgomp1 libstdc++-4.9-dev libstdc++6 libubsan0
14 upgraded, 75 newly installed, 0 to remove and 35 not upgraded.
Need to get 69.0 MB/69.0 MB of archives.
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Get:1 http://172.17.0.1/private/ stretch-staging/main gcc-5-base armhf 5.1.1-5+rpi1 [163 kB]
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Get:4 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.0-1 [24.0 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libssl1.0.0 armhf 1.0.2a-1 [878 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
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Get:10 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.22+15-2 [244 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main libpython2.7-minimal armhf 2.7.10~rc1-1 [379 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main mime-support all 3.58 [36.0 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libexpat1 armhf 2.1.0-6 [60.2 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.1-2 [18.1 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main libsqlite3-0 armhf 3.8.10-1 [385 kB]
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Get:19 http://172.17.0.1/private/ stretch-staging/main python2.7-minimal armhf 2.7.10~rc1-1 [1156 kB]
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Get:34 http://172.17.0.1/private/ stretch-staging/main gcc-4.9-base armhf 4.9.2-16 [161 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.44.0-3 [2399 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main libfreetype6 armhf 2.5.2-4 [412 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main ucf all 3.0030 [69.7 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main fonts-dejavu-core all 2.34-1 [1047 kB]
Get:40 http://172.17.0.1/private/ stretch-staging/main fontconfig-config all 2.11.0-6.3 [273 kB]
Get:41 http://172.17.0.1/private/ stretch-staging/main libfontconfig1 armhf 2.11.0-6.3 [311 kB]
Get:42 http://172.17.0.1/private/ stretch-staging/main libgfortran3 armhf 5.1.1-5+rpi1 [155 kB]
Get:43 http://172.17.0.1/private/ stretch-staging/main libpixman-1-0 armhf 0.32.6-3 [422 kB]
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Get:45 http://172.17.0.1/private/ stretch-staging/main libpython2.7-dev armhf 2.7.10~rc1-1 [17.9 MB]
Get:46 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:47 http://172.17.0.1/private/ stretch-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:48 http://172.17.0.1/private/ stretch-staging/main libxdmcp6 armhf 1:1.1.2-1 [25.0 kB]
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Get:53 http://172.17.0.1/private/ stretch-staging/main libxcb-shm0 armhf 1.10-3 [11.0 kB]
Get:54 http://172.17.0.1/private/ stretch-staging/main libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:55 http://172.17.0.1/private/ stretch-staging/main libxrender1 armhf 1:0.9.8-1 [30.4 kB]
Get:56 http://172.17.0.1/private/ stretch-staging/main libxslt1.1 armhf 1.1.28-2+b1 [213 kB]
Get:57 http://172.17.0.1/private/ stretch-staging/main sgml-base all 1.26+nmu4 [14.6 kB]
Get:58 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.22+15-2 [59.9 kB]
Get:59 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.3-2 [116 kB]
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Get:62 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:63 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:64 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150507 [824 kB]
Get:65 http://172.17.0.1/private/ stretch-staging/main xml-core all 0.13+nmu2 [24.2 kB]
Get:66 http://172.17.0.1/private/ stretch-staging/main sgml-data all 2.0.10 [181 kB]
Get:67 http://172.17.0.1/private/ stretch-staging/main docbook-xml all 4.5-7.2 [347 kB]
Get:68 http://172.17.0.1/private/ stretch-staging/main docbook-xsl all 1.78.1+dfsg-1 [2339 kB]
Get:69 http://172.17.0.1/private/ stretch-staging/main gcc armhf 4:4.9.2-3 [5126 B]
Get:70 http://172.17.0.1/private/ stretch-staging/main libgfortran-4.9-dev armhf 4.9.2-16 [179 kB]
Get:71 http://172.17.0.1/private/ stretch-staging/main gfortran-4.9 armhf 4.9.2-16 [4525 kB]
Get:72 http://172.17.0.1/private/ stretch-staging/main gfortran armhf 4:4.9.2-3 [1294 B]
Get:73 http://172.17.0.1/private/ stretch-staging/main libblas-common armhf 1.2.20110419-10 [8494 B]
Get:74 http://172.17.0.1/private/ stretch-staging/main libblas3 armhf 1.2.20110419-10 [120 kB]
Get:75 http://172.17.0.1/private/ stretch-staging/main libcairo2 armhf 1.14.2-2 [672 kB]
Get:76 http://172.17.0.1/private/ stretch-staging/main liblapack3 armhf 3.5.0-4 [1316 kB]
Get:77 http://172.17.0.1/private/ stretch-staging/main libopenbabel4 armhf 2.3.2+dfsg-2 [2488 kB]
Get:78 http://172.17.0.1/private/ stretch-staging/main libpython-dev armhf 2.7.9-1 [19.6 kB]
Get:79 http://172.17.0.1/private/ stretch-staging/main libxml2-utils armhf 2.9.1+dfsg1-5 [89.4 kB]
Get:80 http://172.17.0.1/private/ stretch-staging/main openbabel armhf 2.3.2+dfsg-2 [248 kB]
Get:81 http://172.17.0.1/private/ stretch-staging/main python2.7-dev armhf 2.7.10~rc1-1 [279 kB]
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Get:83 http://172.17.0.1/private/ stretch-staging/main python-numpy armhf 1:1.8.2-2 [1498 kB]
Get:84 http://172.17.0.1/private/ stretch-staging/main scons all 2.3.1-2 [518 kB]
Get:85 http://172.17.0.1/private/ stretch-staging/main swig2.0 armhf 2.0.12-1 [1071 kB]
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Get:87 http://172.17.0.1/private/ stretch-staging/main xsltproc armhf 1.1.28-2+b1 [118 kB]
Get:88 http://172.17.0.1/private/ stretch-staging/main xmlto armhf 0.0.25-2 [36.0 kB]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.25 g++-4.9_4.9.2-16 gcc-4.9_4.9.2-16 libc6-dev_2.19-18 libstdc++-4.9-dev_4.9.2-16 libstdc++6_5.1.1-5+rpi1 linux-libc-dev_3.16.7-ckt4-1+rpi1
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.8 base-files_8+rpi1 base-passwd_3.5.37 bash_4.3-11 binutils_2.25-5 bsdmainutils_9.0.6 bsdutils_1:2.25.2-6 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:4.9.2-3 cpp-4.9_4.9.2-16 dash_0.5.7-4 debconf_1.5.56 debconf-i18n_1.5.56 debfoster_2.7-2 debhelper_9.20150507 debianutils_4.4 diffutils_1:3.3-1 dmsetup_2:1.02.90-2.2 docbook-xml_4.5-7.2 docbook-xsl_1.78.1+dfsg-1 dpkg_1.17.25 dpkg-dev_1.17.25 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9 fontconfig-config_2.11.0-6.3 fonts-dejavu-core_2.34-1 g++_4:4.9.2-2 g++-4.9_4.9.2-16 gcc_4:4.9.2-3 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-1 gcc-4.9_4.9.2-16 gcc-4.9-base_4.9.2-16 gcc-5-base_5.1.1-5+rpi1 gettext_0.19.3-2 gettext-base_0.19.3-2 gfortran_4:4.9.2-3 gfortran-4.9_4.9.2-16 gnupg_1.4.18-7 gpgv_1.4.18-7 grep_2.20-4.1 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.15 init_1.22 init-system-helpers_1.22 initramfs-tools_0.120 initscripts_2.88dsf-59 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 klibc-utils_2.0.4-2+rpi1 kmod_18-3 libacl1_2.2.52-2 libapt-pkg4.12_1.0.9.8 libasan1_4.9.2-16 libasprintf0c2_0.19.3-2 libatomic1_5.1.1-5+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1 libblas-common_1.2.20110419-10 libblas3_1.2.20110419-10 libblkid1_2.25.2-6 libbz2-1.0_1.0.6-7 libc-bin_2.19-18 libc-dev-bin_2.19-18 libc6_2.19-18 libc6-dev_2.19-18 libcairo2_1.14.2-2 libcap2_1:2.24-8 libcap2-bin_1:2.24-8 libcloog-isl4_0.18.2-1 libcomerr2_1.42.12-1.1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-9 libdbus-1-3_1.8.16-1 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.2 libdpkg-perl_1.17.25 libdrm2_2.4.58-2 libexpat1_2.1.0-6 libexpat1-dev_2.1.0-6 libfakeroot_1.20.2-1 libffi6_3.1-2 libfontconfig1_2.11.0-6.3 libfreetype6_2.5.2-4 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-16 libgcc1_1:5.1.1-5+rpi1 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libgfortran-4.9-dev_4.9.2-16 libgfortran3_5.1.1-5+rpi1 libglib2.0-0_2.44.0-3 libgmp10_2:6.0.0+dfsg-6+rpi1 libgomp1_5.1.1-5+rpi1 libgpg-error0_1.17-3 libisl10_0.12.2-2 libisl13_0.14-2 libklibc_2.0.4-2+rpi1 libkmod2_18-3 liblapack3_3.5.0-4 liblocale-gettext-perl_1.05-8+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.22+15-2 libmount1_2.25.2-6 libmpc3_1.0.2-1 libmpfr4_3.1.2-2 libncurses5_5.9+20140913-1 libncursesw5_5.9+20140913-1 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libopenbabel4_2.3.2+dfsg-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_2:8.35-3.3 libpipeline1_1.4.0-1 libpixman-1-0_0.32.6-3 libpng12-0_1.2.50-2 libprocps3_2:3.3.9-9 libpython-dev_2.7.9-1 libpython-stdlib_2.7.9-1 libpython2.7_2.7.10~rc1-1 libpython2.7-dev_2.7.10~rc1-1 libpython2.7-minimal_2.7.10~rc1-1 libpython2.7-stdlib_2.7.10~rc1-1 libreadline6_6.3-8 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2 libsmartcols1_2.25.2-6 libsqlite3-0_3.8.10-1 libss2_1.42.12-1.1 libssl1.0.0_1.0.2a-1 libstdc++-4.9-dev_4.9.2-16 libstdc++6_5.1.1-5+rpi1 libsystemd0_215-17 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1 libubsan0_5.1.1-5+rpi1 libudev1_215-17 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3 libuuid1_2.25.2-6 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 libxcb-shm0_1.10-3 libxcb1_1.10-3 libxdmcp6_1:1.1.2-1 libxext6_2:1.3.3-1 libxml2_2.9.1+dfsg1-5 libxml2-utils_2.9.1+dfsg1-5 libxrender1_1:0.9.8-1 libxslt1.1_1.1.28-2+b1 linux-libc-dev_3.16.7-ckt4-1+rpi1 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.1 makedev_2.3.1-93 man-db_2.7.0.2-5 mawk_1.3.3-17 mime-support_3.58 mount_2.25.2-6 mountall_2.54 multiarch-support_2.19-18 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1 openbabel_2.3.2+dfsg-2 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-3 perl-base_5.20.2-3 perl-modules_5.20.2-3 plymouth_0.9.0-9 po-debconf_1.0.18 procps_2:3.3.9-9 python_2.7.9-1 python-dev_2.7.9-1 python-minimal_2.7.9-1 python-numpy_1:1.8.2-2 python2.7_2.7.10~rc1-1 python2.7-dev_2.7.10~rc1-1 python2.7-minimal_2.7.10~rc1-1 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_2.3.1-2 sed_4.2.2-4 sensible-utils_0.0.9 sgml-base_1.26+nmu4 sgml-data_2.0.10 startpar_0.59-3 swig_2.0.12-1 swig2.0_2.0.12-1 systemd_215-17 systemd-sysv_215-17 sysv-rc_2.88dsf-59 sysvinit-utils_2.88dsf-59 tar_1.27.1-2 tzdata_2015c-1 ucf_3.0030 udev_215-17 util-linux_2.25.2-6 xml-core_0.13+nmu2 xmlto_0.0.25-2 xsltproc_1.1.28-2+b1 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon May 18 09:02:22 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-1.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-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=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-95101614-b546-4341-9992-6015ca6e8a2b
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 2.0.0+dfsg-1
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: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
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
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
make[1]: Entering directory '/«BUILDDIR»/pdb2pqr-2.0.0+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-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'
dh_installman -a
dh_python2 -a
W: dh_python2:479: Please add dh-python package to Build-Depends
dh_perl -a
dh_link -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory '/«BUILDDIR»/pdb2pqr-2.0.0+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-2.0.0+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_2.0.0+dfsg-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pdb2pqr_2.0.0+dfsg-1_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 20150524-0525
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
pdb2pqr_2.0.0+dfsg-1_armhf.changes:
───────────────────────────────────
Format: 1.8
Date: Mon, 18 May 2015 09:31:58 +0200
Source: pdb2pqr
Binary: pdb2pqr pdb2pqr-doc
Architecture: armhf
Version: 2.0.0+dfsg-1
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: 772350 785546
Changes:
pdb2pqr (2.0.0+dfsg-1) unstable; urgency=medium
.
* New upstream version
* cme fix dpkg-control
* Fix bashism
Closes: #772350
* Make the build reproducible by preseting URL and PREFIX (thanks for the
patch to Reiner Herrmann <reiner@reiner-h.de>)
Closes: #785546
Checksums-Sha1:
8cf8d0a9ea1baa4c5e10c4e29d088d93d1c28e9c 353282 pdb2pqr_2.0.0+dfsg-1_armhf.deb
Checksums-Sha256:
2d57d96c2dd61676c9e39867be9295c32be04993e520c5d58b80600c8972157b 353282 pdb2pqr_2.0.0+dfsg-1_armhf.deb
Files:
b7fda65ad457d9507a8afe9056e9dcc1 353282 science optional pdb2pqr_2.0.0+dfsg-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
pdb2pqr_2.0.0+dfsg-1_armhf.deb
──────────────────────────────
new debian package, version 2.0.
size 353282 bytes: control archive=5177 bytes.
1361 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-1
Architecture: armhf
Maintainer: Debian Med <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2591
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libpython2.7 (>= 2.7), libstdc++6 (>= 4.3.0), 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 2015-05-24 05:24 ./
drwxr-xr-x root/root 0 2015-05-24 05:24 ./usr/
drwxr-xr-x root/root 0 2015-05-24 05:24 ./usr/bin/
-rwxr-xr-x root/root 124 2015-05-24 05:24 ./usr/bin/pdb2pqr
-rwxr-xr-x root/root 126 2015-05-24 05:24 ./usr/bin/psize
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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 │
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Build Architecture: armhf
Build-Space: 31372
Build-Time: 120
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 546
Job: pdb2pqr_2.0.0+dfsg-1
Machine Architecture: armhf
Package: pdb2pqr
Package-Time: 726
Source-Version: 2.0.0+dfsg-1
Space: 31372
Status: successful
Version: 2.0.0+dfsg-1
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Finished at 20150524-0525
Build needed 00:12:06, 31372k disc space