sbuild (Debian sbuild) 0.63.1 (31 May 2012) on build06.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ pdb2pqr 1.8-1 (armhf) 24 Dec 2012 09:41 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: pdb2pqr Version: 1.8-1 Source Version: 1.8-1 Distribution: wheezy-staging Machine Architecture: armhf Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/pdb2pqr-w21KBz/pdb2pqr-1.8' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/pdb2pqr-w21KBz' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/wheezy-staging-armhf-sbuild-7f94fb1b-92c4-40aa-bf83-a99ce795ce79' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://archive.raspbian.lan wheezy-staging InRelease [9334 B] Get:2 http://archive.raspbian.lan wheezy-staging/main Sources [6233 kB] Get:3 http://archive.raspbian.lan wheezy-staging/main armhf Packages [7393 kB] Ign http://archive.raspbian.lan wheezy-staging/main Translation-en Fetched 13.6 MB in 42s (319 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://svn.debian.org/debian-med/trunk/packages/pdb2pqr/trunk/ Need to get 1941 kB of source archives. Get:1 http://archive.raspbian.lan/raspbian/ wheezy-staging/main pdb2pqr 1.8-1 (dsc) [1546 B] Get:2 http://archive.raspbian.lan/raspbian/ wheezy-staging/main pdb2pqr 1.8-1 (tar) [1929 kB] Get:3 http://archive.raspbian.lan/raspbian/ wheezy-staging/main pdb2pqr 1.8-1 (diff) [10.6 kB] Fetched 1941 kB in 0s (2506 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-KFdywV/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... sbuild-build-depends-core-dummy is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded. Merged Build-Depends: 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, autoconf, automake, libtool, autotools-dev, python-dev, python-numpy Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), gfortran, swig, xmlto, openbabel, autoconf, automake, libtool, autotools-dev, python-dev, python-numpy dpkg-deb: building package `sbuild-build-depends-pdb2pqr-dummy' in `/«BUILDDIR»/resolver-2l4Nwt/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: autoconf automake autotools-dev docbook-xml docbook-xsl fontconfig-config gfortran gfortran-4.6 libblas3 libblas3gf libcairo2 libexpat1 libexpat1-dev libfontconfig1 libfreetype6 libgcrypt11 libgfortran3 libgpg-error0 liblapack3 liblapack3gf libncursesw5 libopenbabel4 libpixman-1-0 libpng12-0 libpython2.7 libsqlite3-0 libssl-dev libssl1.0.0 libtool libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxml2-utils libxrender1 libxslt1.1 m4 mime-support openbabel python python-dev python-minimal python-numpy python-support python2.7 python2.7-dev python2.7-minimal sgml-base sgml-data swig swig2.0 ttf-dejavu-core xml-core xmlto xsltproc zlib1g-dev Suggested packages: autoconf2.13 autoconf-archive gnu-standards autoconf-doc docbook docbook-dsssl docbook-defguide docbook-xsl-doc-html docbook-xsl-doc-pdf docbook-xsl-doc-text docbook-xsl-doc libsaxon-java libxalan2-java libxslthl-java docbook-xsl-saxon fop xalan dbtoepub gfortran-doc gfortran-4.6-doc libgfortran3-dbg rng-tools libtool-doc automaken gcj python-doc python-tk python-numpy-doc python-numpy-dbg python-nose python2.7-doc binfmt-support sgml-base-doc perlsgml w3-recs opensp swig-doc swig-examples swig2.0-examples swig2.0-doc w3m lynx-cur links xmltex Recommended packages: libgpm2 libssl-doc libltdl-dev libpaper-utils zip The following NEW packages will be installed: autoconf automake autotools-dev docbook-xml docbook-xsl fontconfig-config gfortran gfortran-4.6 libblas3 libblas3gf libcairo2 libexpat1 libexpat1-dev libfontconfig1 libfreetype6 libgcrypt11 libgfortran3 libgpg-error0 liblapack3 liblapack3gf libncursesw5 libopenbabel4 libpixman-1-0 libpng12-0 libpython2.7 libsqlite3-0 libssl-dev libssl1.0.0 libtool libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxml2-utils libxrender1 libxslt1.1 m4 mime-support openbabel python python-dev python-minimal python-numpy python-support python2.7 python2.7-dev python2.7-minimal sbuild-build-depends-pdb2pqr-dummy sgml-base sgml-data swig swig2.0 ttf-dejavu-core xml-core xmlto xsltproc zlib1g-dev 0 upgraded, 60 newly installed, 0 to remove and 32 not upgraded. Need to get 8821 kB/64.5 MB of archives. After this operation, 140 MB of additional disk space will be used. Get:1 http://archive.raspbian.lan/raspbian/ wheezy-staging/main gfortran-4.6 armhf 4.6.3-12+rpi1 [4830 kB] Get:2 http://archive.raspbian.lan/raspbian/ wheezy-staging/main gfortran armhf 4:4.6.3-8 [1134 B] Get:3 http://archive.raspbian.lan/raspbian/ wheezy-staging/main libopenbabel4 armhf 2.3.1+dfsg-4 [3714 kB] Get:4 http://archive.raspbian.lan/raspbian/ wheezy-staging/main openbabel armhf 2.3.1+dfsg-4 [276 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 8821 kB in 2s (3539 kB/s) Selecting previously unselected package libncursesw5:armhf. (Reading database ... 12360 files and directories currently installed.) Unpacking libncursesw5:armhf (from .../libncursesw5_5.9-10_armhf.deb) ... Selecting previously unselected package libssl1.0.0:armhf. Unpacking libssl1.0.0:armhf (from .../libssl1.0.0_1.0.1c-4+rpi1_armhf.deb) ... 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Setting up libgpg-error0:armhf (1.10-3.1) ... Setting up libgcrypt11:armhf (1.5.0-3) ... Setting up libsqlite3-0:armhf (3.7.13-1) ... Setting up sgml-data (2.0.8) ... Setting up libexpat1:armhf (2.1.0-1) ... Setting up libfreetype6:armhf (2.4.9-1) ... Setting up ttf-dejavu-core (2.33-3) ... Setting up fontconfig-config (2.9.0-7.1) ... Setting up libfontconfig1:armhf (2.9.0-7.1) ... Setting up libpixman-1-0:armhf (0.26.0-3) ... Setting up libpng12-0:armhf (1.2.49-1) ... Setting up libxau6:armhf (1:1.0.7-1) ... Setting up libxdmcp6:armhf (1:1.1.1-1) ... Setting up libxcb1:armhf (1.8.1-2) ... Setting up libx11-data (2:1.5.0-1) ... Setting up libx11-6:armhf (2:1.5.0-1) ... Setting up libxcb-render0:armhf (1.8.1-2) ... Setting up libxcb-shm0:armhf (1.8.1-2) ... Setting up libxrender1:armhf (1:0.9.7-1) ... Setting up libcairo2:armhf (1.12.2-2) ... Setting up libgfortran3:armhf (4.7.2-4+rpi1) ... Setting up libxslt1.1:armhf (1.1.26-14) ... Setting up m4 (1.4.16-3) ... Setting up mime-support (3.52-1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up python2.7-minimal (2.7.3~rc2-2.1) ... Setting up python2.7 (2.7.3~rc2-2.1) ... Setting up python-minimal (2.7.3~rc2-1) ... Setting up python (2.7.3~rc2-1) ... Setting up python-support (1.0.15) ... Setting up autoconf (2.69-1) ... Setting up autotools-dev (20120608.1) ... Setting up automake (1:1.11.6-1) ... update-alternatives: using /usr/bin/automake-1.11 to provide /usr/bin/automake (automake) in auto mode Setting up docbook-xsl (1.76.1+dfsg-1) ... Setting up gfortran-4.6 (4.6.3-12+rpi1) ... Setting up gfortran (4:4.6.3-8) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode Setting up libblas3 (1.2.20110419-5) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libblas3gf (1.2.20110419-5) ... Setting up libexpat1-dev (2.1.0-1) ... Setting up liblapack3 (3.4.1-6) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up liblapack3gf (3.4.1-6) ... Setting up libopenbabel4 (2.3.1+dfsg-4) ... Setting up libpython2.7 (2.7.3~rc2-2.1) ... Setting up zlib1g-dev:armhf (1:1.2.7.dfsg-13) ... Setting up libssl-dev (1.0.1c-4+rpi1) ... Setting up libtool (2.4.2-1.1) ... Setting up libxml2-utils (2.8.0+dfsg1-7) ... Setting up openbabel (2.3.1+dfsg-4) ... Setting up python2.7-dev (2.7.3~rc2-2.1) ... Setting up python-dev (2.7.3~rc2-1) ... Setting up python-numpy (1:1.6.2-1) ... Setting up swig2.0 (2.0.7-3) ... Setting up swig (2.0.7-3) ... Setting up xsltproc (1.1.26-14) ... Processing triggers for sgml-base ... Updating the super catalog... Setting up docbook-xml (4.5-7.1) ... Processing triggers for sgml-base ... Updating the super catalog... Setting up xmlto (0.0.25-2) ... Setting up sbuild-build-depends-pdb2pqr-dummy (0.invalid.0) ... Processing triggers for python-support ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-2-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-12+rpi1 gcc-4.6_4.6.3-12+rpi1 libc6-dev_2.13-35 libstdc++6_4.7.2-4+rpi1 libstdc++6-4.6-dev_4.6.3-12+rpi1 linux-libc-dev_3.2.21-1+rpi1 Package versions: apt_0.9.3+rpi1 autoconf_2.69-1 automake_1:1.11.6-1 autotools-dev_20120608.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-4 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5+b1 bzip2_1.0.6-4 coreutils_8.13-3.2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12+rpi1 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debianutils_4.3.2 diffutils_1:3.2-6 docbook-xml_4.5-7.1 docbook-xsl_1.76.1+dfsg-1 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 eatmydata_26-2 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 fontconfig-config_2.9.0-7.1 g++_4:4.6.3-7 g++-4.6_4.6.3-12+rpi1 gcc_4:4.6.3-8 gcc-4.4-base_4.4.7-1.1+rpi1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-12+rpi1 gcc-4.6-base_4.6.3-12+rpi1 gcc-4.7-base_4.7.2-4+rpi1 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gfortran_4:4.6.3-8 gfortran-4.6_4.6.3-12+rpi1 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hardening-wrapper_2.2 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.3+rpi1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblas3_1.2.20110419-5 libblas3gf_1.2.20110419-5 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libcairo2_1.12.2-2 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libconfig-dev_1.4.8-5 libconfig9_1.4.8-5 libcroco3_0.6.6-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libexpat1_2.1.0-1 libexpat1-dev_2.1.0-1 libffi5_3.0.10-3+b3 libfontconfig1_2.9.0-7.1 libfreetype6_2.4.9-1 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4+rpi1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libgfortran3_4.7.2-4+rpi1 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4+rpi1 libgpg-error0_1.10-3.1 libio-socket-inet6-perl_2.69-2 liblapack3_3.4.1-6 liblapack3gf_3.4.1-6 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libopenbabel4_2.3.1+dfsg-4 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libpixman-1-0_0.26.0-3 libpng12-0_1.2.49-1 libpopt0_1.16-7 libpython2.7_2.7.3~rc2-2.1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libsocket6-perl_0.23-1 libsqlite3-0_3.7.13-1 libss2_1.42.5-1 libssl-dev_1.0.1c-4+rpi1 libssl1.0.0_1.0.1c-4+rpi1 libstdc++6_4.7.2-4+rpi1 libstdc++6-4.6-dev_4.6.3-12+rpi1 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libtool_2.4.2-1.1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libwrap0_7.6.q-24 libwrap0-dev_7.6.q-24 libx11-6_2:1.5.0-1 libx11-data_2:1.5.0-1 libxau6_1:1.0.7-1 libxcb-render0_1.8.1-2 libxcb-shm0_1.8.1-2 libxcb1_1.8.1-2 libxdmcp6_1:1.1.1-1 libxml2_2.8.0+dfsg1-7 libxml2-utils_2.8.0+dfsg1-7 libxrender1_1:0.9.7-1 libxslt1.1_1.1.26-14 linux-libc-dev_3.2.21-1+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 m4_1.4.16-3 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mime-support_3.52-1 mount_2.20.1-5.2 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 openbabel_2.3.1+dfsg-4 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15+rpi1 perl-base_5.14.2-15+rpi1 perl-modules_5.14.2-15+rpi1 pkg-config_0.26-1 po-debconf_1.0.16+nmu2 psmisc_22.19-1 python_2.7.3~rc2-1 python-dev_2.7.3~rc2-1 python-minimal_2.7.3~rc2-1 python-numpy_1:1.6.2-1 python-support_1.0.15 python2.7_2.7.3~rc2-2.1 python2.7-dev_2.7.3~rc2-2.1 python2.7-minimal_2.7.3~rc2-2.1 raspbian-archive-keyring_20120528.2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pdb2pqr-dummy_0.invalid.0 sbuild-build-depends-sslh-dummy_0.invalid.0 sed_4.2.1-10 sensible-utils_0.0.7 sgml-base_1.26+nmu3 sgml-data_2.0.8 swig_2.0.7-3 swig2.0_2.0.7-3 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 ttf-dejavu-core_2.33-3 tzdata_2012g-1 ucf_3.0025+nmu3 util-linux_2.20.1-5.2 xml-core_0.13+nmu2 xmlto_0.0.25-2 xsltproc_1.1.26-14 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Thu Jun 21 15:17:41 2012 UTC using DSA key ID CC8D7957 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./pdb2pqr_1.8-1.dsc dpkg-source: info: extracting pdb2pqr in pdb2pqr-1.8 dpkg-source: info: unpacking pdb2pqr_1.8.orig.tar.gz dpkg-source: info: unpacking pdb2pqr_1.8-1.debian.tar.gz dpkg-source: info: applying fix-includes.patch dpkg-source: info: applying fix-hashbangs.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LD_PRELOAD=/usr/lib/libeatmydata/libeatmydata.so LOGNAME=buildd PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/games PWD=/«PKGBUILDDIR» SCHROOT_ALIAS_NAME=chroot:wheezy-staging-armhf-sbuild SCHROOT_CHROOT_NAME=wheezy-staging-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=wheezy-staging-armhf-sbuild-7f94fb1b-92c4-40aa-bf83-a99ce795ce79 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package pdb2pqr dpkg-buildpackage: source version 1.8-1 dpkg-source --before-build pdb2pqr-1.8 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 `/«PKGBUILDDIR»' ( 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 ) dh_auto_clean make[1]: Leaving directory `/«PKGBUILDDIR»' dh_clean debian/rules build-arch dh build-arch --with python2 dh_testdir -a debian/rules override_dh_auto_configure make[1]: Entering directory `/«PKGBUILDDIR»' dh_auto_configure -- CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/usr/share/pyshared/numpy/core/include/numpy" CPPFLAGS="-D_FORTIFY_SOURCE=2 -fPIC -I/usr/share/pyshared/numpy/core/include/numpy" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/usr/share/pyshared/numpy/core/include/numpy" FFLAGS="-g -O2 -fPIC" LDFLAGS="-Wl,-z,relro" checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking target system type... arm-unknown-linux-gnueabihf checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for g++... g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... none checking for python... /usr/bin/python checking for python include directory... -I/usr/include/python2.7 checking for--disable-pdb2pka... no ------------- Begin Processing pdb2pka Configure Options ----------- checking whether you defined Numeric or Numpy... no checking for Numeric include files... no checking whether you defined numpy... no /usr/bin/python: can't open file './contrib/numpy-1.1.0/setup.py': [Errno 2] No such file or directory checking for numpy includes files... -I/usr/numpy/lib/python2.7/site-packages/numpy/core/include/numpy ------------- End Processing pdb2ka Configure Options ----------- checking for tmp/... no checking for OpenBabel... OpenBabel found in /usr/bin/babel, you can use OpenBabel to generate MOL2 files. ------------- End Processing PDB2PQR Configure Options ----------- configure: creating ./config.status config.status: creating Makefile config.status: creating pdb2pka/Makefile config.status: creating pdb2pka/substruct/Makefile config.status: creating tests/Makefile config.status: creating tests/test/Makefile config.status: creating tests/adv-test/Makefile config.status: creating tests/test-long/Makefile config.status: creating tests/test-webserver/Makefile config.status: creating tests/local-test/Makefile config.status: executing depfiles commands --------------------------------------------------------------------------------------- Please run "make" followed by "make install" to complete the installation. You may also run "make test" or "make adv-test". ======================== Configuration Parameters ======================== User ID: buildd Version: 1.8 Install Dir: /usr/ pdb2pka: enable PY_CFLAGS: -I/usr/include/python2.7 -I/usr/numpy/lib/python2.7/site-packages/numpy/core/include/numpy WEBSITE (path to the website directory): http://build06.raspbian.lan/pdb2pqr/ (WEBSITE can be changed with the --with-url option) PDB2PQR_CGI (path to pdb2pqr.cgi): http://build06.raspbian.lan/pdb2pqr/pdb2pqr.cgi PDB2PQR jobs will be forked on the server MAX_ATOMS (max number of atoms in a protein): 10000 As a regular user, you must ask your system administrator to create a symbolic link that enables you to view http://build06.raspbian.lan/pdb2pqr/ after you run "make install" ( 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 `/«PKGBUILDDIR»' dh_auto_build -a make[1]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu Making all in pdb2pka make[2]: Entering directory `/«PKGBUILDDIR»/pdb2pka' cd .. && make am--refresh make[3]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[3]: Leaving directory `/«PKGBUILDDIR»' make[3]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[3]: Leaving directory `/«PKGBUILDDIR»' Making all in substruct make[3]: Entering directory `/«PKGBUILDDIR»/pdb2pka/substruct' cd ../.. && make am--refresh make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.8\" -DPACKAGE_STRING=\"PDB2PQR\ 1.8\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.8\" -I. -D_FORTIFY_SOURCE=2 -fPIC -I/usr/share/pyshared/numpy/core/include/numpy -I/usr/include/python2.7 -I/usr/numpy/lib/python2.7/site-packages/numpy/core/include/numpy -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/usr/share/pyshared/numpy/core/include/numpy -c -o Algorithms.o Algorithms.cpp In file included from /usr/include/python2.7/Python.h:8:0, from Algorithms.cpp:40: /usr/include/python2.7/pyconfig.h:1161:0: warning: "_POSIX_C_SOURCE" redefined [enabled by default] /usr/include/features.h:163:0: note: this is the location of the previous definition /usr/include/python2.7/pyconfig.h:1183:0: warning: "_XOPEN_SOURCE" redefined [enabled by default] /usr/include/features.h:165:0: note: this is the location of the previous definition g++ -o Algorithms.so -shared Algorithms.o make[3]: Leaving directory `/«PKGBUILDDIR»/pdb2pka/substruct' make[3]: Entering directory `/«PKGBUILDDIR»/pdb2pka' cd .. && make am--refresh make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.8\" -DPACKAGE_STRING=\"PDB2PQR\ 1.8\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.8\" -I. -D_FORTIFY_SOURCE=2 -fPIC -I/usr/share/pyshared/numpy/core/include/numpy -I/usr/include/python2.7 -I/usr/numpy/lib/python2.7/site-packages/numpy/core/include/numpy -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/usr/share/pyshared/numpy/core/include/numpy -c -o pMC_mult.o pMC_mult.cpp g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.8\" -DPACKAGE_STRING=\"PDB2PQR\ 1.8\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.8\" -I. -D_FORTIFY_SOURCE=2 -fPIC -I/usr/share/pyshared/numpy/core/include/numpy -I/usr/include/python2.7 -I/usr/numpy/lib/python2.7/site-packages/numpy/core/include/numpy -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/usr/share/pyshared/numpy/core/include/numpy -c -o pMC_mult_wrap.o pMC_mult_wrap.cpp g++ -o _pMC_mult.so -shared pMC_mult.o pMC_mult_wrap.o make[3]: Leaving directory `/«PKGBUILDDIR»/pdb2pka' make[2]: Leaving directory `/«PKGBUILDDIR»/pdb2pka' Making all in tests make[2]: Entering directory `/«PKGBUILDDIR»/tests' cd .. && make am--refresh make[3]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[3]: Leaving directory `/«PKGBUILDDIR»' make[3]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[3]: Leaving directory `/«PKGBUILDDIR»' Making all in test make[3]: Entering directory `/«PKGBUILDDIR»/tests/test' cd ../.. && make am--refresh make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' Making all in . make[4]: Entering directory `/«PKGBUILDDIR»/tests/test' cd ../.. && make am--refresh make[5]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[5]: Leaving directory `/«PKGBUILDDIR»' make[5]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[5]: Leaving directory `/«PKGBUILDDIR»' g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.8\" -DPACKAGE_STRING=\"PDB2PQR\ 1.8\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.8\" -I. -D_FORTIFY_SOURCE=2 -fPIC -I/usr/share/pyshared/numpy/core/include/numpy -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/usr/share/pyshared/numpy/core/include/numpy -c -o test.o test.cpp test.cpp: In function 'int main()': test.cpp:36:60: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] test.cpp:39:57: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] test.cpp:52:68: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] test.cpp:103:110: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] test.cpp:106:119: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/usr/share/pyshared/numpy/core/include/numpy -Wl,-z,relro -o simpletest test.o make[4]: Leaving directory `/«PKGBUILDDIR»/tests/test' make[3]: Leaving directory `/«PKGBUILDDIR»/tests/test' Making all in adv-test make[3]: Entering directory `/«PKGBUILDDIR»/tests/adv-test' cd ../.. && make am--refresh make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' Making all in . make[4]: Entering directory `/«PKGBUILDDIR»/tests/adv-test' cd ../.. && make am--refresh make[5]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[5]: Leaving directory `/«PKGBUILDDIR»' make[5]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[5]: Leaving directory `/«PKGBUILDDIR»' g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.8\" -DPACKAGE_STRING=\"PDB2PQR\ 1.8\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.8\" -I. -D_FORTIFY_SOURCE=2 -fPIC -I/usr/share/pyshared/numpy/core/include/numpy -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/usr/share/pyshared/numpy/core/include/numpy -c -o test.o test.cpp test.cpp: In function 'int main()': test.cpp:44:57: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] test.cpp:47:60: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] test.cpp:59:66: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] test.cpp:84:112: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] test.cpp:87:121: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] test.cpp:98:70: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] test.cpp:119:124: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] test.cpp:122:116: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/usr/share/pyshared/numpy/core/include/numpy -Wl,-z,relro -o advtest test.o make[4]: Leaving directory `/«PKGBUILDDIR»/tests/adv-test' make[3]: Leaving directory `/«PKGBUILDDIR»/tests/adv-test' Making all in test-long make[3]: Entering directory `/«PKGBUILDDIR»/tests/test-long' cd ../.. && make am--refresh make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' Making all in . make[4]: Entering directory `/«PKGBUILDDIR»/tests/test-long' cd ../.. && make am--refresh make[5]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[5]: Leaving directory `/«PKGBUILDDIR»' make[5]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[5]: Leaving directory `/«PKGBUILDDIR»' make[4]: Nothing to be done for `all-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/tests/test-long' make[3]: Leaving directory `/«PKGBUILDDIR»/tests/test-long' Making all in local-test make[3]: Entering directory `/«PKGBUILDDIR»/tests/local-test' cd ../.. && make am--refresh make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' Making all in . make[4]: Entering directory `/«PKGBUILDDIR»/tests/local-test' cd ../.. && make am--refresh make[5]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[5]: Leaving directory `/«PKGBUILDDIR»' make[5]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[5]: Leaving directory `/«PKGBUILDDIR»' g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.8\" -DPACKAGE_STRING=\"PDB2PQR\ 1.8\" -DPACKAGE_BUGREPORT=\"baker@biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.8\" -I. -D_FORTIFY_SOURCE=2 -fPIC -I/usr/share/pyshared/numpy/core/include/numpy -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/usr/share/pyshared/numpy/core/include/numpy -c -o test.o test.cpp test.cpp: In function 'int main()': test.cpp:36:60: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] test.cpp:39:57: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] test.cpp:52:68: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] test.cpp:103:109: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] test.cpp:106:118: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fPIC -I/usr/share/pyshared/numpy/core/include/numpy -Wl,-z,relro -o localtest test.o make[4]: Leaving directory `/«PKGBUILDDIR»/tests/local-test' make[3]: Leaving directory `/«PKGBUILDDIR»/tests/local-test' Making all in test-webserver make[3]: Entering directory `/«PKGBUILDDIR»/tests/test-webserver' cd ../.. && make am--refresh make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' Making all in . make[4]: Entering directory `/«PKGBUILDDIR»/tests/test-webserver' cd ../.. && make am--refresh make[5]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[5]: Leaving directory `/«PKGBUILDDIR»' make[5]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[5]: Leaving directory `/«PKGBUILDDIR»' make[4]: Nothing to be done for `all-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/tests/test-webserver' make[3]: Leaving directory `/«PKGBUILDDIR»/tests/test-webserver' Making all in . make[3]: Entering directory `/«PKGBUILDDIR»/tests' cd .. && make am--refresh make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' make[4]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[4]: Leaving directory `/«PKGBUILDDIR»' make[3]: Nothing to be done for `all-am'. make[3]: Leaving directory `/«PKGBUILDDIR»/tests' make[2]: Leaving directory `/«PKGBUILDDIR»/tests' make[2]: Entering directory `/«PKGBUILDDIR»' cd . && : cd . && : --gnu make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' 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 `/«PKGBUILDDIR»' 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 `/«PKGBUILDDIR»' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_installcatalogs -a dh_installcron -a dh_installdebconf -a dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_installgsettings -a dh_bugfiles -a dh_ucf -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_python2 -a dh_usrlocal -a dh_link -a dh_compress -a debian/rules override_dh_fixperms make[1]: Entering directory `/«PKGBUILDDIR»' 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 0755 debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py make[1]: Leaving directory `/«PKGBUILDDIR»' 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 dpkg-gencontrol: warning: package pdb2pqr: unknown substitution variable ${python:Versions} dh_md5sums -a dh_builddeb -a dpkg-deb: building package `pdb2pqr' in `../pdb2pqr_1.8-1_armhf.deb'. dpkg-genchanges -B -mbuildd >../pdb2pqr_1.8-1_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-1.8 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20121224-0948 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ pdb2pqr_1.8-1_armhf.changes: ──────────────────────────── Format: 1.8 Date: Thu, 21 Jun 2012 16:21:50 +0200 Source: pdb2pqr Binary: pdb2pqr pdb2pqr-doc Architecture: armhf Version: 1.8-1 Distribution: wheezy-staging Urgency: low Maintainer: buildd Changed-By: Manuel Prinz Description: pdb2pqr - Preparation of protein structures for electrostatics calculations pdb2pqr-doc - example files accompanying pdb2pqr Closes: 654240 Changes: pdb2pqr (1.8-1) unstable; urgency=low . [ Andreas Tille ] * debian/upstream: Add publication information . [ Manuel Prinz ] * New upstream version. Updated debian/copyright. * Updated Standards-Version to 3.9.3. No changes needed. * Changed Maintainer to Debian Med team. * Pass -fPIC to CXXFLAGS. Thanks to Konstantinos Margaritis for the patch! Closes: 654240. LP: 935357. * Updated PROPKA packaging to new version. (It's written in Python now.) * Added fix-hashbangs.patch. * Merged pdb2pqr and propka packages as they are more interconnected since this upstream version. Updated README.Debian accordingly. Checksums-Sha1: 1a92797eaa665be8a23e2e76360aadf875913100 450386 pdb2pqr_1.8-1_armhf.deb Checksums-Sha256: 24561dbb4fc7a3ba272f675f742fc9da90ea095fd42b692d39cce8d4cb630271 450386 pdb2pqr_1.8-1_armhf.deb Files: 4a37214e10db79bb294b82e1961b4c5a 450386 science optional pdb2pqr_1.8-1_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ pdb2pqr_1.8-1_armhf.deb ─────────────────────── new debian package, version 2.0. size 450386 bytes: control archive=4744 bytes. 1345 bytes, 29 lines control 9027 bytes, 124 lines md5sums 182 bytes, 9 lines * postinst #!/bin/sh 251 bytes, 14 lines * prerm #!/bin/sh Package: pdb2pqr Version: 1.8-1 Architecture: armhf Maintainer: Debian Med Installed-Size: 2337 Depends: libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), python (>= 2.6.6-7~), python2.7, python-numpy Suggests: apbs Enhances: autodocktools Conflicts: propka 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 2012-12-24 09:47 ./ drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/ drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/share/ drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/share/pdb2pqr/ drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/share/pdb2pqr/dat/ -rw-r--r-- root/root 24406 2010-03-29 08:16 ./usr/share/pdb2pqr/dat/PARSE.DAT -rw-r--r-- root/root 64231 2008-05-06 09:32 ./usr/share/pdb2pqr/dat/CHARMM.DAT -rw-r--r-- root/root 60679 2007-11-07 08:36 ./usr/share/pdb2pqr/dat/AMBER.DAT -rw-r--r-- root/root 29525 2008-03-24 06:57 ./usr/share/pdb2pqr/dat/PEOEPB.DAT -rw-r--r-- root/root 58175 2010-12-16 09:02 ./usr/share/pdb2pqr/dat/AA.xml -rw-r--r-- root/root 62119 2010-12-16 09:02 ./usr/share/pdb2pqr/dat/TOPOLOGY.xml -rw-r--r-- root/root 97563 2007-03-17 07:14 ./usr/share/pdb2pqr/dat/TYL06.DAT -rw-r--r-- root/root 1993 2008-06-20 11:05 ./usr/share/pdb2pqr/dat/TYL06.names -rw-r--r-- root/root 4484 2010-12-16 09:02 ./usr/share/pdb2pqr/dat/HYDROGENS.xml -rw-r--r-- root/root 15457 2010-12-16 09:02 ./usr/share/pdb2pqr/dat/PATCHES.xml -rw-r--r-- root/root 1672 2008-03-25 10:03 ./usr/share/pdb2pqr/dat/PEOEPB.names -rw-r--r-- root/root 5692 2010-03-29 08:16 ./usr/share/pdb2pqr/dat/PARSE.names -rw-r--r-- root/root 33835 2010-12-16 09:02 ./usr/share/pdb2pqr/dat/NA.xml -rw-r--r-- root/root 2290 2008-06-20 11:05 ./usr/share/pdb2pqr/dat/AMBER.names -rw-r--r-- root/root 34200 2009-11-05 08:33 ./usr/share/pdb2pqr/dat/SWANSON.DAT -rw-r--r-- root/root 6846 2009-02-02 13:22 ./usr/share/pdb2pqr/dat/CHARMM.names -rw-r--r-- root/root 1185 2009-11-05 08:33 ./usr/share/pdb2pqr/dat/SWANSON.names -rwxr-xr-x root/root 3077 2012-12-24 09:45 ./usr/share/pdb2pqr/pdb2pqr.py drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/share/pdb2pqr/propka30/ -rw-r--r-- root/root 3565 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/propka_det.py drwxr-xr-x root/root 0 2012-12-24 09:44 ./usr/share/pdb2pqr/propka30/Source/ -rw-r--r-- root/root 15315 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/iterative.py -rw-r--r-- root/root 55687 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/parameters.py -rw-r--r-- root/root 26298 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/lib.py -rw-r--r-- root/root 16272 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/coupled_residues.py -rw-r--r-- root/root 31136 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/residue.py -rw-r--r-- root/root 16664 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/parameters_new.py -rw-r--r-- root/root 19367 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/protonate.py -rw-r--r-- root/root 12071 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/vector_algebra.py -rw-r--r-- root/root 20807 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/bonds.py -rw-r--r-- root/root 6370 2012-12-24 09:44 ./usr/share/pdb2pqr/propka30/Source/corresponding_atoms.py -rw-r--r-- root/root 13935 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/determinants.py -rw-r--r-- root/root 13102 2012-12-24 09:44 ./usr/share/pdb2pqr/propka30/Source/rotate.py -rw-r--r-- root/root 2787 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/determinant.py -rw-r--r-- root/root 35409 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/protein.py -rw-r--r-- root/root 2599 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/__init__.py -rw-r--r-- root/root 53168 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/mutate.py -rw-r--r-- root/root 6738 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/debug.py -rw-r--r-- root/root 19278 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/pdb.py -rw-r--r-- root/root 16262 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/parameters_std.py -rw-r--r-- root/root 19167 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/calculator.py -rw-r--r-- root/root 18323 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/output.py -rw-r--r-- root/root 14857 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/chain.py -rw-r--r-- root/root 3405 2011-08-03 17:29 ./usr/share/pdb2pqr/propka30/Source/protein_bonds.dat -rw-r--r-- root/root 12445 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/compare.py -rw-r--r-- root/root 26326 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/protonator.py -rw-r--r-- root/root 59438 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/version.py -rw-r--r-- root/root 16724 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/Source/ligand.py -rw-r--r-- root/root 447 2011-08-03 17:29 ./usr/share/pdb2pqr/propka30/Source/ions.list -rw-r--r-- root/root 4055 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/propka_mut.py -rw-r--r-- root/root 2978 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/propka_pdb.py -rw-r--r-- root/root 2404 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/__init__.py -rwxr-xr-x root/root 3039 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/propka.py -rw-r--r-- root/root 12583 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/experiment.py -rw-r--r-- root/root 7147 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/compare.py -rw-r--r-- root/root 3987 2012-01-16 17:53 ./usr/share/pdb2pqr/propka30/propka_gui.py drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/share/pdb2pqr/extensions/ -rw-r--r-- root/root 3055 2012-01-16 17:53 ./usr/share/pdb2pqr/extensions/salt.py -rw-r--r-- root/root 3219 2012-01-16 17:53 ./usr/share/pdb2pqr/extensions/template -rw-r--r-- root/root 6986 2012-01-16 17:53 ./usr/share/pdb2pqr/extensions/hbond.py -rw-r--r-- root/root 944 2012-01-16 17:53 ./usr/share/pdb2pqr/extensions/summary.py -rw-r--r-- root/root 4628 2012-01-16 17:53 ./usr/share/pdb2pqr/extensions/__init__.py -rw-r--r-- root/root 12373 2012-01-16 17:53 ./usr/share/pdb2pqr/extensions/resinter.py -rw-r--r-- root/root 1941 2012-01-16 17:53 ./usr/share/pdb2pqr/extensions/chi.py -rw-r--r-- root/root 3339 2012-01-16 17:53 ./usr/share/pdb2pqr/extensions/rama.py -rw-r--r-- root/root 206 2006-04-28 09:11 ./usr/share/pdb2pqr/extensions/README -rw-r--r-- root/root 2843 2012-01-16 17:53 ./usr/share/pdb2pqr/extensions/contact.py -rw-r--r-- root/root 26035 2012-01-24 16:33 ./usr/share/pdb2pqr/main_cgi.py drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/share/pdb2pqr/pdb2pka/ -rwxr-xr-x root/root 11421 2012-12-24 09:44 ./usr/share/pdb2pqr/pdb2pka/inputgen_pKa.py drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/share/pdb2pqr/pdb2pka/substruct/ -rw-r--r-- root/root 7 2011-06-10 05:32 ./usr/share/pdb2pqr/pdb2pka/substruct/__init__.py -rwxr-xr-x root/root 8043 2011-03-30 07:35 ./usr/share/pdb2pqr/pdb2pka/prepare_pKa_ligand.py drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/share/pdb2pqr/pdb2pka/ligandclean/ -rw-r--r-- root/root 4703 2006-03-24 06:51 ./usr/share/pdb2pqr/pdb2pka/ligandclean/trial_templates.py -rw-r--r-- root/root 26 2011-03-30 07:35 ./usr/share/pdb2pqr/pdb2pka/ligandclean/__init__.py -rw-r--r-- root/root 1004 2006-03-24 06:51 ./usr/share/pdb2pqr/pdb2pka/ligandclean/lookuptable.py -rw-r--r-- root/root 13279 2012-01-16 17:53 ./usr/share/pdb2pqr/pdb2pka/ligandclean/ligff.py -rw-r--r-- root/root 3969 2006-03-24 06:51 ./usr/share/pdb2pqr/pdb2pka/ligandclean/templates.py -rw-r--r-- root/root 5164 2007-01-30 17:03 ./usr/share/pdb2pqr/pdb2pka/ligandclean/peoe_PDB2PQR.py -rw-r--r-- root/root 7906 2006-12-05 17:35 ./usr/share/pdb2pqr/pdb2pka/example.py -rw-r--r-- root/root 28527 2011-08-30 17:07 ./usr/share/pdb2pqr/pdb2pka/NEWligand_topology.py -rw-r--r-- root/root 13419 2012-12-24 09:45 ./usr/share/pdb2pqr/pdb2pka/pMC_mult.py -rwxr-xr-x root/root 21701 2012-01-11 08:23 ./usr/share/pdb2pqr/pdb2pka/pka.py -rw-r--r-- root/root 0 2006-12-09 07:59 ./usr/share/pdb2pqr/pdb2pka/__init__.py -rw-r--r-- root/root 98915 2012-01-11 08:23 ./usr/share/pdb2pqr/pdb2pka/pka_routines.py -rw-r--r-- root/root 4081 2010-07-23 07:32 ./usr/share/pdb2pqr/pdb2pka/pka_help.py -rw-r--r-- root/root 13792 2011-06-10 08:48 ./usr/share/pdb2pqr/pdb2pka/apbs.py -rw-r--r-- root/root 28449 2008-06-13 07:15 ./usr/share/pdb2pqr/pdb2pka/ligand_topology.py -rw-r--r-- root/root 4910 2009-04-22 12:43 ./usr/share/pdb2pqr/pdb2pka/pKa_base.py -rw-r--r-- root/root 5498 2009-04-22 12:43 ./usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py -rw-r--r-- root/root 34195 2009-04-22 12:43 ./usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py -rw-r--r-- root/root 3425 2010-01-29 03:27 ./usr/share/pdb2pqr/pdb2pka/charge_mon.py drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/share/pdb2pqr/src/ -rw-r--r-- root/root 18094 2010-12-16 09:02 ./usr/share/pdb2pqr/src/inputgen.py -rw-r--r-- root/root 3220 2010-12-16 09:02 ./usr/share/pdb2pqr/src/aconf.py.in -rw-r--r-- root/root 3226 2012-12-24 09:45 ./usr/share/pdb2pqr/src/aconf.py -rw-r--r-- root/root 14825 2010-12-16 09:02 ./usr/share/pdb2pqr/src/topology.py -rw-r--r-- root/root 15573 2010-12-16 09:02 ./usr/share/pdb2pqr/src/quatfit.py -rw-r--r-- root/root 103973 2012-01-16 17:53 ./usr/share/pdb2pqr/src/hydrogens.py -rw-r--r-- root/root 18515 2012-12-24 09:45 ./usr/share/pdb2pqr/src/server.py -rw-r--r-- root/root 18515 2011-08-03 14:14 ./usr/share/pdb2pqr/src/server.py.in -rwxr-xr-x root/root 18240 2010-12-16 09:02 ./usr/share/pdb2pqr/src/psize.py -rw-r--r-- root/root 9408 2012-01-16 17:53 ./usr/share/pdb2pqr/src/na.py -rw-r--r-- root/root 28462 2012-01-20 12:25 ./usr/share/pdb2pqr/src/structures.py -rw-r--r-- root/root 13103 2012-01-16 17:53 ./usr/share/pdb2pqr/src/protein.py -rw-r--r-- root/root 67846 2012-01-16 17:53 ./usr/share/pdb2pqr/src/routines.py -rw-r--r-- root/root 0 2005-04-22 09:03 ./usr/share/pdb2pqr/src/__init__.py -rw-r--r-- root/root 16516 2012-01-23 17:28 ./usr/share/pdb2pqr/src/utilities.py -rw-r--r-- root/root 106390 2012-01-16 17:53 ./usr/share/pdb2pqr/src/pdb.py -rw-r--r-- root/root 25009 2012-01-16 17:53 ./usr/share/pdb2pqr/src/aa.py -rw-r--r-- root/root 35008 2012-01-16 17:53 ./usr/share/pdb2pqr/src/forcefield.py -rw-r--r-- root/root 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-rw-r--r-- root/root 5439 2012-06-21 07:21 ./usr/share/doc/pdb2pqr/copyright -rw-r--r-- root/root 183 2009-10-21 12:12 ./usr/share/doc/pdb2pqr/README -rw-r--r-- root/root 489 2012-06-21 07:21 ./usr/share/doc/pdb2pqr/README.Debian drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/share/python/ drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/share/python/runtime.d/ -rwxr-xr-x root/root 136 2012-12-24 09:47 ./usr/share/python/runtime.d/pdb2pqr.rtupdate drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/bin/ -rwxr-xr-x root/root 124 2012-12-24 09:47 ./usr/bin/pdb2pqr -rwxr-xr-x root/root 126 2012-12-24 09:47 ./usr/bin/psize -rwxr-xr-x root/root 132 2012-12-24 09:47 ./usr/bin/propka drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/lib/ drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/lib/pdb2pqr/ drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/lib/pdb2pqr/pdb2pka/ drwxr-xr-x root/root 0 2012-12-24 09:47 ./usr/lib/pdb2pqr/pdb2pka/substruct/ -rw-r--r-- root/root 10784 2012-12-24 09:47 ./usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.so -rw-r--r-- root/root 232404 2012-12-24 09:47 ./usr/lib/pdb2pqr/pdb2pka/_pMC_mult.so lrwxrwxrwx root/root 0 2012-12-24 09:47 ./usr/share/pdb2pqr/pdb2pka/substruct/Algorithms.so -> ../../../../lib/pdb2pqr/pdb2pka/substruct/Algorithms.so lrwxrwxrwx root/root 0 2012-12-24 09:47 ./usr/share/pdb2pqr/pdb2pka/_pMC_mult.so -> ../../../lib/pdb2pqr/pdb2pka/_pMC_mult.so ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: autoconf* automake* autotools-dev* docbook-xml* docbook-xsl* fontconfig-config* gfortran* gfortran-4.6* libblas3* libblas3gf* libcairo2* libexpat1* libexpat1-dev* libfontconfig1* libfreetype6* libgcrypt11* libgfortran3* libgpg-error0* liblapack3* liblapack3gf* libncursesw5* libopenbabel4* libpixman-1-0* libpng12-0* libpython2.7* libsqlite3-0* libssl-dev* libssl1.0.0* libtool* libx11-6* libx11-data* libxau6* libxcb-render0* libxcb-shm0* libxcb1* libxdmcp6* libxml2-utils* libxrender1* libxslt1.1* m4* mime-support* openbabel* python* python-dev* python-minimal* python-numpy* python-support* python2.7* python2.7-dev* python2.7-minimal* sbuild-build-depends-pdb2pqr-dummy* sgml-base* sgml-data* swig* swig2.0* ttf-dejavu-core* xml-core* xmlto* xsltproc* zlib1g-dev* 0 upgraded, 0 newly installed, 60 to remove and 32 not upgraded. After this operation, 140 MB disk space will be freed. (Reading database ... 16852 files and directories currently installed.) Removing sbuild-build-depends-pdb2pqr-dummy ... Removing automake ... Removing autoconf ... Purging configuration files for autoconf ... Removing libtool ... Removing autotools-dev ... Removing xmlto ... Removing docbook-xml ... Purging configuration files for docbook-xml ... Removing docbook-xsl ... Purging configuration files for docbook-xsl ... Removing openbabel ... Removing libopenbabel4 ... Purging configuration files for libopenbabel4 ... Removing libcairo2:armhf ... Purging configuration files for libcairo2:armhf ... Removing libfontconfig1:armhf ... Purging configuration files for libfontconfig1:armhf ... Removing fontconfig-config ... Purging configuration files for fontconfig-config ... Removing gfortran ... Removing gfortran-4.6 ... Removing python-numpy ... Removing liblapack3gf ... Removing liblapack3 ... Purging configuration files for liblapack3 ... Removing libblas3gf ... Removing libblas3 ... Removing python-dev ... Removing python2.7-dev ... Removing python-support ... Purging configuration files for python-support ... Removing python ... Purging configuration files for python ... Removing libpython2.7 ... Purging configuration files for libpython2.7 ... Removing python2.7 ... Purging configuration files for python2.7 ... Removing libexpat1-dev ... Removing libexpat1:armhf ... Purging configuration files for libexpat1:armhf ... Removing libfreetype6:armhf ... Purging configuration files for libfreetype6:armhf ... Removing xsltproc ... Removing libxslt1.1:armhf ... Purging configuration files for libxslt1.1:armhf ... Removing libgcrypt11:armhf ... Purging configuration files for libgcrypt11:armhf ... Removing libgfortran3:armhf ... Purging configuration files for libgfortran3:armhf ... Removing libgpg-error0:armhf ... Purging configuration files for libgpg-error0:armhf ... Removing libncursesw5:armhf ... Purging configuration files for libncursesw5:armhf ... Removing libpixman-1-0:armhf ... Purging configuration files for libpixman-1-0:armhf ... Removing libpng12-0:armhf ... Purging configuration files for libpng12-0:armhf ... Removing libsqlite3-0:armhf ... Purging configuration files for libsqlite3-0:armhf ... Removing libssl-dev ... Removing python-minimal ... Removing python2.7-minimal ... Purging configuration files for python2.7-minimal ... Removing libssl1.0.0:armhf ... Purging configuration files for libssl1.0.0:armhf ... Removing libxrender1:armhf ... Purging configuration files for libxrender1:armhf ... Removing libx11-6:armhf ... Purging configuration files for libx11-6:armhf ... Removing libx11-data ... Removing libxcb-shm0:armhf ... Purging configuration files for libxcb-shm0:armhf ... Removing libxcb-render0:armhf ... Purging configuration files for libxcb-render0:armhf ... Removing libxcb1:armhf ... Purging configuration files for libxcb1:armhf ... Removing libxau6:armhf ... Purging configuration files for libxau6:armhf ... Removing libxdmcp6:armhf ... Purging configuration files for libxdmcp6:armhf ... Removing libxml2-utils ... Removing m4 ... Removing mime-support ... Purging configuration files for mime-support ... Removing sgml-data ... Purging configuration files for sgml-data ... Removing xml-core ... Purging configuration files for xml-core ... dpkg: warning: while removing xml-core, directory '/etc/sgml' not empty so not removed Removing sgml-base ... Purging configuration files for sgml-base ... Removing swig ... Removing swig2.0 ... Removing ttf-dejavu-core ... Removing zlib1g-dev:armhf ... Processing triggers for man-db ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: armhf Build-Space: 17136 Build-Time: 224 Distribution: wheezy-staging Host Architecture: armhf Install-Time: 118 Job: pdb2pqr_1.8-1 Machine Architecture: armhf Package: pdb2pqr Package-Time: 404 Source-Version: 1.8-1 Space: 17136 Status: successful Version: 1.8-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20121224-0948 Build needed 00:06:44, 17136k disc space