RUN: /bin/echo ['echo', 'Forking build subprocess...'] Forking build subprocess... RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'ccc6d0ce9756546b6d2bdf229438d70f02628f08', '/home/buildd/filecache-default/185546b3f9e19debe6e8eae994b2de1aab1a184f'] Synching the system clock with the buildd NTP service... 3 Sep 13:19:08 ntpdate[25951]: adjust time server 10.211.37.1 offset 0.000012 sec Unpacking chroot for build ccc6d0ce9756546b6d2bdf229438d70f02628f08 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'ccc6d0ce9756546b6d2bdf229438d70f02628f08'] Mounting chroot for build ccc6d0ce9756546b6d2bdf229438d70f02628f08 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'ccc6d0ce9756546b6d2bdf229438d70f02628f08', 'deb http://ftpmaster.internal/ubuntu oneiric main universe'] Overriding sources.list in build-ccc6d0ce9756546b6d2bdf229438d70f02628f08 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'ccc6d0ce9756546b6d2bdf229438d70f02628f08', 'armel'] Updating debian chroot for build ccc6d0ce9756546b6d2bdf229438d70f02628f08 Ign http://ftpmaster.internal oneiric InRelease Get:1 http://ftpmaster.internal oneiric Release.gpg [198 B] Get:2 http://ftpmaster.internal oneiric Release [39.8 kB] Get:3 http://ftpmaster.internal oneiric/main armel Packages [1557 kB] Get:4 http://ftpmaster.internal oneiric/universe armel Packages [6292 kB] Ign http://ftpmaster.internal oneiric/main TranslationIndex Ign http://ftpmaster.internal oneiric/universe TranslationIndex Fetched 7890 kB in 47s (166 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: libtinfo5 The following packages will be upgraded: busybox-initramfs ca-certificates cpp-4.6 fakeroot g++-4.6 gcc-4.6 gcc-4.6-base ifupdown klibc-utils libc-bin libc-dev-bin libc6 libc6-dev libdbus-1-3 libffi6 libgcc1 libglib2.0-0 libgnutls26 libgomp1 libklibc libncurses5 libncursesw5 libpam-modules libpam-modules-bin libpam-runtime libpam0g libreadline6 libstdc++6 libstdc++6-4.6-dev libudev0 linux-libc-dev lockfile-progs lsb-base multiarch-support ncurses-base ncurses-bin pkgbinarymangler readline-common udev 39 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 26.9 MB of archives. After this operation, 201 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libc-dev-bin libc6-dev libc-bin libc6 linux-libc-dev libgomp1 gcc-4.6-base libgcc1 cpp-4.6 libstdc++6-4.6-dev g++-4.6 gcc-4.6 libstdc++6 libtinfo5 ncurses-bin ncurses-base libpam0g libpam-modules-bin libpam-modules libdbus-1-3 libffi6 libglib2.0-0 libudev0 libgnutls26 readline-common libreadline6 libncurses5 libpam-runtime lsb-base multiarch-support lockfile-progs busybox-initramfs ifupdown klibc-utils libklibc libncursesw5 udev ca-certificates fakeroot pkgbinarymangler Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ oneiric/main libc-dev-bin armel 2.13-17ubuntu2 [72.7 kB] Get:2 http://ftpmaster.internal/ubuntu/ oneiric/main libc6-dev armel 2.13-17ubuntu2 [2216 kB] Get:3 http://ftpmaster.internal/ubuntu/ oneiric/main libc-bin armel 2.13-17ubuntu2 [844 kB] Get:4 http://ftpmaster.internal/ubuntu/ oneiric/main libc6 armel 2.13-17ubuntu2 [3857 kB] Get:5 http://ftpmaster.internal/ubuntu/ oneiric/main linux-libc-dev armel 3.0.0-10.16 [801 kB] Get:6 http://ftpmaster.internal/ubuntu/ oneiric/main libgomp1 armel 4.6.1-7ubuntu2 [23.6 kB] Get:7 http://ftpmaster.internal/ubuntu/ oneiric/main gcc-4.6-base armel 4.6.1-7ubuntu2 [16.5 kB] Get:8 http://ftpmaster.internal/ubuntu/ oneiric/main libgcc1 armel 1:4.6.1-7ubuntu2 [22.2 kB] Get:9 http://ftpmaster.internal/ubuntu/ oneiric/main cpp-4.6 armel 4.6.1-7ubuntu2 [4047 kB] Get:10 http://ftpmaster.internal/ubuntu/ oneiric/main libstdc++6-4.6-dev armel 4.6.1-7ubuntu2 [1694 kB] Get:11 http://ftpmaster.internal/ubuntu/ oneiric/main g++-4.6 armel 4.6.1-7ubuntu2 [4910 kB] Get:12 http://ftpmaster.internal/ubuntu/ oneiric/main gcc-4.6 armel 4.6.1-7ubuntu2 [4512 kB] Get:13 http://ftpmaster.internal/ubuntu/ oneiric/main libstdc++6 armel 4.6.1-7ubuntu2 [274 kB] Get:14 http://ftpmaster.internal/ubuntu/ oneiric/main libtinfo5 armel 5.9-1ubuntu3 [57.0 kB] Get:15 http://ftpmaster.internal/ubuntu/ oneiric/main ncurses-bin armel 5.9-1ubuntu3 [145 kB] Get:16 http://ftpmaster.internal/ubuntu/ oneiric/main ncurses-base all 5.9-1ubuntu3 [20.2 kB] Get:17 http://ftpmaster.internal/ubuntu/ oneiric/main libpam0g armel 1.1.3-2ubuntu1 [48.7 kB] Get:18 http://ftpmaster.internal/ubuntu/ oneiric/main libpam-modules-bin armel 1.1.3-2ubuntu1 [28.7 kB] Get:19 http://ftpmaster.internal/ubuntu/ oneiric/main libpam-modules armel 1.1.3-2ubuntu1 [243 kB] Get:20 http://ftpmaster.internal/ubuntu/ oneiric/main libdbus-1-3 armel 1.4.14-1ubuntu1 [116 kB] Get:21 http://ftpmaster.internal/ubuntu/ oneiric/main libffi6 armel 3.0.11~rc1-2 [16.8 kB] Get:22 http://ftpmaster.internal/ubuntu/ oneiric/main libglib2.0-0 armel 2.29.18-0ubuntu3 [1009 kB] Get:23 http://ftpmaster.internal/ubuntu/ oneiric/main libudev0 armel 173-0ubuntu3 [26.9 kB] Get:24 http://ftpmaster.internal/ubuntu/ oneiric/main libgnutls26 armel 2.10.5-1ubuntu3 [379 kB] Get:25 http://ftpmaster.internal/ubuntu/ oneiric/main readline-common all 6.2-2ubuntu1 [49.8 kB] Get:26 http://ftpmaster.internal/ubuntu/ oneiric/main libreadline6 armel 6.2-2ubuntu1 [112 kB] Get:27 http://ftpmaster.internal/ubuntu/ oneiric/main libncurses5 armel 5.9-1ubuntu3 [112 kB] Get:28 http://ftpmaster.internal/ubuntu/ oneiric/main libpam-runtime armel 1.1.3-2ubuntu1 [44.8 kB] Get:29 http://ftpmaster.internal/ubuntu/ oneiric/main lsb-base all 4.0-0ubuntu15 [10.6 kB] Get:30 http://ftpmaster.internal/ubuntu/ oneiric/main multiarch-support armel 2.13-17ubuntu2 [4486 B] Get:31 http://ftpmaster.internal/ubuntu/ oneiric/main lockfile-progs armel 0.1.15ubuntu1 [9458 B] Get:32 http://ftpmaster.internal/ubuntu/ oneiric/main busybox-initramfs armel 1:1.18.4-2ubuntu2 [154 kB] Get:33 http://ftpmaster.internal/ubuntu/ oneiric/main ifupdown armel 0.7~alpha5.1ubuntu4 [43.0 kB] Get:34 http://ftpmaster.internal/ubuntu/ oneiric/main klibc-utils armel 1.5.22-1ubuntu2 [192 kB] Get:35 http://ftpmaster.internal/ubuntu/ oneiric/main libklibc armel 1.5.22-1ubuntu2 [46.9 kB] Get:36 http://ftpmaster.internal/ubuntu/ oneiric/main libncursesw5 armel 5.9-1ubuntu3 [133 kB] Get:37 http://ftpmaster.internal/ubuntu/ oneiric/main udev armel 173-0ubuntu3 [298 kB] Get:38 http://ftpmaster.internal/ubuntu/ oneiric/main ca-certificates armel 20110502+nmu1 [165 kB] Get:39 http://ftpmaster.internal/ubuntu/ oneiric/main fakeroot armel 1.17-1 [72.6 kB] Get:40 http://ftpmaster.internal/ubuntu/ oneiric/main pkgbinarymangler all 102 [26.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 26.9 MB in 10s (2488 kB/s) (Reading database ... 13961 files and directories currently installed.) Preparing to replace libc-dev-bin 2.13-16ubuntu4 (using .../libc-dev-bin_2.13-17ubuntu2_armel.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libc6-dev 2.13-16ubuntu4 (using .../libc6-dev_2.13-17ubuntu2_armel.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-bin 2.13-16ubuntu4 (using .../libc-bin_2.13-17ubuntu2_armel.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.13-17ubuntu2) ... (Reading database ... 13961 files and directories currently installed.) Preparing to replace libc6 2.13-16ubuntu4 (using .../libc6_2.13-17ubuntu2_armel.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.13-17ubuntu2) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 13961 files and directories currently installed.) Preparing to replace linux-libc-dev 3.0.0-8.11 (using .../linux-libc-dev_3.0.0-10.16_armel.deb) ... Unpacking replacement linux-libc-dev ... Preparing to replace libgomp1 4.6.1-7ubuntu1 (using .../libgomp1_4.6.1-7ubuntu2_armel.deb) ... Unpacking replacement libgomp1 ... Preparing to replace gcc-4.6-base 4.6.1-7ubuntu1 (using .../gcc-4.6-base_4.6.1-7ubuntu2_armel.deb) ... Unpacking replacement gcc-4.6-base ... Setting up gcc-4.6-base (4.6.1-7ubuntu2) ... (Reading database ... 13964 files and directories currently installed.) Preparing to replace libgcc1 1:4.6.1-7ubuntu1 (using .../libgcc1_1%3a4.6.1-7ubuntu2_armel.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.6.1-7ubuntu2) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 13964 files and directories currently installed.) Preparing to replace cpp-4.6 4.6.1-7ubuntu1 (using .../cpp-4.6_4.6.1-7ubuntu2_armel.deb) ... Unpacking replacement cpp-4.6 ... Preparing to replace libstdc++6-4.6-dev 4.6.1-7ubuntu1 (using .../libstdc++6-4.6-dev_4.6.1-7ubuntu2_armel.deb) ... Unpacking replacement libstdc++6-4.6-dev ... Preparing to replace g++-4.6 4.6.1-7ubuntu1 (using .../g++-4.6_4.6.1-7ubuntu2_armel.deb) ... Unpacking replacement g++-4.6 ... Preparing to replace gcc-4.6 4.6.1-7ubuntu1 (using .../gcc-4.6_4.6.1-7ubuntu2_armel.deb) ... Unpacking replacement gcc-4.6 ... Preparing to replace libstdc++6 4.6.1-7ubuntu1 (using .../libstdc++6_4.6.1-7ubuntu2_armel.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.6.1-7ubuntu2) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Selecting previously deselected package libtinfo5. (Reading database ... 13961 files and directories currently installed.) Unpacking libtinfo5 (from .../libtinfo5_5.9-1ubuntu3_armel.deb) ... Setting up libtinfo5 (5.9-1ubuntu3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 13966 files and directories currently installed.) Preparing to replace ncurses-bin 5.9-1 (using .../ncurses-bin_5.9-1ubuntu3_armel.deb) ... Unpacking replacement ncurses-bin ... Setting up ncurses-bin (5.9-1ubuntu3) ... (Reading database ... 13966 files and directories currently installed.) Preparing to replace ncurses-base 5.9-1 (using .../ncurses-base_5.9-1ubuntu3_all.deb) ... Unpacking replacement ncurses-base ... Setting up ncurses-base (5.9-1ubuntu3) ... (Reading database ... 13966 files and directories currently installed.) Preparing to replace libpam0g 1.1.3-1ubuntu3 (using .../libpam0g_1.1.3-2ubuntu1_armel.deb) ... Unpacking replacement libpam0g ... Setting up libpam0g (1.1.3-2ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 13966 files and directories currently installed.) Preparing to replace libpam-modules-bin 1.1.3-1ubuntu3 (using .../libpam-modules-bin_1.1.3-2ubuntu1_armel.deb) ... Unpacking replacement libpam-modules-bin ... Setting up libpam-modules-bin (1.1.3-2ubuntu1) ... (Reading database ... 13966 files and directories currently installed.) Preparing to replace libpam-modules 1.1.3-1ubuntu3 (using .../libpam-modules_1.1.3-2ubuntu1_armel.deb) ... Unpacking replacement libpam-modules ... Setting up libpam-modules (1.1.3-2ubuntu1) ... (Reading database ... 13966 files and directories currently installed.) Preparing to replace libdbus-1-3 1.4.12-4ubuntu2 (using .../libdbus-1-3_1.4.14-1ubuntu1_armel.deb) ... Unpacking replacement libdbus-1-3 ... Preparing to replace libffi6 3.0.10~rc8-6 (using .../libffi6_3.0.11~rc1-2_armel.deb) ... Unpacking replacement libffi6 ... Preparing to replace libglib2.0-0 2.29.16-0ubuntu2 (using .../libglib2.0-0_2.29.18-0ubuntu3_armel.deb) ... Unpacking replacement libglib2.0-0 ... Preparing to replace libudev0 173-0ubuntu1 (using .../libudev0_173-0ubuntu3_armel.deb) ... Unpacking replacement libudev0 ... Preparing to replace libgnutls26 2.10.5-1ubuntu2 (using .../libgnutls26_2.10.5-1ubuntu3_armel.deb) ... Unpacking replacement libgnutls26 ... Preparing to replace readline-common 6.2-2 (using .../readline-common_6.2-2ubuntu1_all.deb) ... Unpacking replacement readline-common ... Setting up readline-common (6.2-2ubuntu1) ... (Reading database ... 13966 files and directories currently installed.) Preparing to replace libreadline6 6.2-2 (using .../libreadline6_6.2-2ubuntu1_armel.deb) ... Unpacking replacement libreadline6 ... Setting up libreadline6 (6.2-2ubuntu1) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 13966 files and directories currently installed.) Preparing to replace libncurses5 5.9-1 (using .../libncurses5_5.9-1ubuntu3_armel.deb) ... Unpacking replacement libncurses5 ... Setting up libncurses5 (5.9-1ubuntu3) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place (Reading database ... 13966 files and directories currently installed.) Preparing to replace libpam-runtime 1.1.3-1ubuntu3 (using .../libpam-runtime_1.1.3-2ubuntu1_armel.deb) ... Unpacking replacement libpam-runtime ... Setting up libpam-runtime (1.1.3-2ubuntu1) ... (Reading database ... 13966 files and directories currently installed.) Preparing to replace lsb-base 4.0-0ubuntu14 (using .../lsb-base_4.0-0ubuntu15_all.deb) ... Unpacking replacement lsb-base ... Setting up lsb-base (4.0-0ubuntu15) ... (Reading database ... 13966 files and directories currently installed.) Preparing to replace multiarch-support 2.13-16ubuntu4 (using .../multiarch-support_2.13-17ubuntu2_armel.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.13-17ubuntu2) ... (Reading database ... 13966 files and directories currently installed.) Preparing to replace lockfile-progs 0.1.15 (using .../lockfile-progs_0.1.15ubuntu1_armel.deb) ... Unpacking replacement lockfile-progs ... Preparing to replace busybox-initramfs 1:1.18.4-2ubuntu1 (using .../busybox-initramfs_1%3a1.18.4-2ubuntu2_armel.deb) ... Unpacking replacement busybox-initramfs ... Preparing to replace ifupdown 0.7~alpha5.1ubuntu2 (using .../ifupdown_0.7~alpha5.1ubuntu4_armel.deb) ... Unpacking replacement ifupdown ... Preparing to replace klibc-utils 1.5.22-1ubuntu1 (using .../klibc-utils_1.5.22-1ubuntu2_armel.deb) ... Unpacking replacement klibc-utils ... Preparing to replace libklibc 1.5.22-1ubuntu1 (using .../libklibc_1.5.22-1ubuntu2_armel.deb) ... Unpacking replacement libklibc ... Preparing to replace libncursesw5 5.9-1 (using .../libncursesw5_5.9-1ubuntu3_armel.deb) ... Unpacking replacement libncursesw5 ... Preparing to replace udev 173-0ubuntu1 (using .../udev_173-0ubuntu3_armel.deb) ... Adding 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' Unpacking replacement udev ... Preparing to replace ca-certificates 20110502 (using .../ca-certificates_20110502+nmu1_armel.deb) ... Unpacking replacement ca-certificates ... Preparing to replace fakeroot 1.16-1 (using .../fakeroot_1.17-1_armel.deb) ... Unpacking replacement fakeroot ... Preparing to replace pkgbinarymangler 101 (using .../pkgbinarymangler_102_all.deb) ... Unpacking replacement pkgbinarymangler ... Setting up libc-dev-bin (2.13-17ubuntu2) ... Setting up linux-libc-dev (3.0.0-10.16) ... Setting up libc6-dev (2.13-17ubuntu2) ... Setting up libgomp1 (4.6.1-7ubuntu2) ... Setting up cpp-4.6 (4.6.1-7ubuntu2) ... Setting up gcc-4.6 (4.6.1-7ubuntu2) ... Setting up libdbus-1-3 (1.4.14-1ubuntu1) ... Setting up libffi6 (3.0.11~rc1-2) ... Setting up libglib2.0-0 (2.29.18-0ubuntu3) ... Setting up libudev0 (173-0ubuntu3) ... Setting up libgnutls26 (2.10.5-1ubuntu3) ... Setting up lockfile-progs (0.1.15ubuntu1) ... Setting up busybox-initramfs (1:1.18.4-2ubuntu2) ... Setting up ifupdown (0.7~alpha5.1ubuntu4) ... Installing new version of config file /etc/network/if-up.d/upstart ... Installing new version of config file /etc/init/network-interface.conf ... Installing new version of config file /etc/init/networking.conf ... Setting up libklibc (1.5.22-1ubuntu2) ... Setting up klibc-utils (1.5.22-1ubuntu2) ... Setting up libncursesw5 (5.9-1ubuntu3) ... Setting up udev (173-0ubuntu3) ... Removing 'diversion of /sbin/udevadm to /sbin/udevadm.upgrade by fake-udev' update-initramfs: deferring update (trigger activated) Setting up ca-certificates (20110502+nmu1) ... Updating certificates in /etc/ssl/certs... WARNING: Skipping duplicate certificate ca-certificates.crt WARNING: Skipping duplicate certificate ca-certificates.crt WARNING: Skipping duplicate certificate IGC_A.pem WARNING: Skipping duplicate certificate IGC_A.pem 0 added, 1 removed; done. Running hooks in /etc/ca-certificates/update.d....done. Setting up fakeroot (1.17-1) ... Setting up pkgbinarymangler (102) ... Setting up g++-4.6 (4.6.1-7ubuntu2) ... Setting up libstdc++6-4.6-dev (4.6.1-7ubuntu2) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Processing triggers for initramfs-tools ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'ccc6d0ce9756546b6d2bdf229438d70f02628f08', 'armel', 'oneiric', '--nolog', '--batch', '--archive=ubuntu', '--dist=oneiric', '--purpose=PRIMARY', '--architecture=armel', '--comp=universe', 'pdb2pqr_1.7-1.dsc'] Initiating build ccc6d0ce9756546b6d2bdf229438d70f02628f08 with 0 processor cores. Automatic build of pdb2pqr_1.7-1 on buttercup by sbuild/armel 1.170.5 Build started at 20110903-1324 ****************************************************************************** pdb2pqr_1.7-1.dsc exists in cwd sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 7.0.50~), gfortran, swig, xmlto, openbabel, python-support, python-dev, python-numpy, autoconf, automake, libtool, autotools-dev sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) sh: gcc: not found dpkg-architecture: warning: Couldn't determine gcc system type, falling back to default (native compilation) Checking for already installed source dependencies... debhelper: missing gfortran: missing swig: missing xmlto: missing openbabel: missing python-support: missing python-dev: missing python-numpy: missing autoconf: missing automake: missing libtool: missing autotools-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper gfortran swig xmlto openbabel python-support python-dev python-numpy autoconf automake libtool autotools-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils docbook-xml docbook-xsl file gettext gettext-base gfortran-4.6 groff-base html2text intltool-debian libblas3gf libcroco3 libdb4.8 libexpat1 libexpat1-dev libgfortran3 liblapack3gf libmagic1 libopenbabel4 libpipeline1 libpython2.7 libsqlite3-0 libssl-dev libunistring0 libxml2 libxml2-utils libxslt1.1 m4 man-db mime-support po-debconf python python2.7 python2.7-dev sgml-base sgml-data xml-core xsltproc zlib1g-dev Suggested packages: autoconf2.13 autoconf-archive gnu-standards autoconf-doc wamerican wordlist whois vacation dh-make docbook docbook-dsssl docbook-defguide docbook-xsl-doc-html docbook-xsl-doc-pdf docbook-xsl-doc-text docbook-xsl-doc libsaxon-java libxalan2-java docbook-xsl-saxon fop xalan dbtoepub gettext-doc gfortran-multilib gfortran-doc gfortran-4.6-multilib gfortran-4.6-doc libgfortran3-dbg groff libtool-doc automaken gcj less www-browser libmail-box-perl python-doc python-tk python-numpy-doc python-numpy-dbg python-nose python2.7-doc sgml-base-doc perlsgml doc-html-w3 opensp swig-examples swig-doc xmltex Recommended packages: curl wget lynx-cur libssl-doc libltdl-dev libmail-sendmail-perl libpaper-utils The following NEW packages will be installed: autoconf automake autotools-dev bsdmainutils debhelper docbook-xml docbook-xsl file gettext gettext-base gfortran gfortran-4.6 groff-base html2text intltool-debian libblas3gf libcroco3 libdb4.8 libexpat1 libexpat1-dev libgfortran3 liblapack3gf libmagic1 libopenbabel4 libpipeline1 libpython2.7 libsqlite3-0 libssl-dev libtool libunistring0 libxml2 libxml2-utils libxslt1.1 m4 man-db mime-support openbabel po-debconf python python-dev python-numpy python-support python2.7 python2.7-dev sgml-base sgml-data swig xml-core xmlto xsltproc zlib1g-dev 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. Need to get 32.8 MB of archives. After this operation, 110 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libdb4.8 libexpat1 libsqlite3-0 libpipeline1 sgml-base xml-core sgml-data docbook-xml libgfortran3 libmagic1 file mime-support python2.7 python bsdmainutils gettext-base groff-base libxml2 man-db m4 autoconf autotools-dev automake html2text libcroco3 libunistring0 gettext intltool-debian po-debconf debhelper docbook-xsl gfortran-4.6 gfortran libblas3gf libexpat1-dev liblapack3gf libopenbabel4 libpython2.7 zlib1g-dev libssl-dev libtool libxml2-utils libxslt1.1 openbabel python2.7-dev python-dev python-support python-numpy swig xsltproc xmlto Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ oneiric/main libdb4.8 armel 4.8.30-9 [581 kB] Get:2 http://ftpmaster.internal/ubuntu/ oneiric/main libexpat1 armel 2.0.1-7ubuntu3 [103 kB] Get:3 http://ftpmaster.internal/ubuntu/ oneiric/main libsqlite3-0 armel 3.7.7-2ubuntu1 [280 kB] Get:4 http://ftpmaster.internal/ubuntu/ oneiric/main libpipeline1 armel 1.2.0-3 [20.6 kB] Get:5 http://ftpmaster.internal/ubuntu/ oneiric/main sgml-base all 1.26+nmu1ubuntu1 [8360 B] Get:6 http://ftpmaster.internal/ubuntu/ oneiric/main xml-core all 0.13 [23.4 kB] Get:7 http://ftpmaster.internal/ubuntu/ oneiric/main sgml-data all 2.0.6 [271 kB] Get:8 http://ftpmaster.internal/ubuntu/ oneiric/main docbook-xml all 4.5-7 [345 kB] Get:9 http://ftpmaster.internal/ubuntu/ oneiric/main libgfortran3 armel 4.6.1-7ubuntu2 [222 kB] Get:10 http://ftpmaster.internal/ubuntu/ oneiric/main libmagic1 armel 5.04-5ubuntu3 [199 kB] Get:11 http://ftpmaster.internal/ubuntu/ oneiric/main file armel 5.04-5ubuntu3 [19.5 kB] Get:12 http://ftpmaster.internal/ubuntu/ oneiric/main mime-support all 3.51-1ubuntu1 [30.7 kB] Get:13 http://ftpmaster.internal/ubuntu/ oneiric/main python2.7 armel 2.7.2-5 [2511 kB] Get:14 http://ftpmaster.internal/ubuntu/ oneiric/main python all 2.7.2-5ubuntu1 [165 kB] Get:15 http://ftpmaster.internal/ubuntu/ oneiric/main bsdmainutils armel 8.2.3 [194 kB] Get:16 http://ftpmaster.internal/ubuntu/ oneiric/main gettext-base armel 0.18.1.1-3ubuntu1 [56.1 kB] Get:17 http://ftpmaster.internal/ubuntu/ oneiric/main groff-base armel 1.21-6 [934 kB] Get:18 http://ftpmaster.internal/ubuntu/ oneiric/main libxml2 armel 2.7.8.dfsg-4 [559 kB] Get:19 http://ftpmaster.internal/ubuntu/ oneiric/main man-db armel 2.6.0.2-2 [675 kB] Get:20 http://ftpmaster.internal/ubuntu/ oneiric/main m4 armel 1.4.16-1 [182 kB] Get:21 http://ftpmaster.internal/ubuntu/ oneiric/main autoconf all 2.68-1ubuntu1 [560 kB] Get:22 http://ftpmaster.internal/ubuntu/ oneiric/main autotools-dev all 20110511.1 [44.7 kB] Get:23 http://ftpmaster.internal/ubuntu/ oneiric/main automake all 1:1.11.1-1ubuntu1 [544 kB] Get:24 http://ftpmaster.internal/ubuntu/ oneiric/main html2text armel 1.3.2a-15 [94.3 kB] Get:25 http://ftpmaster.internal/ubuntu/ oneiric/main libcroco3 armel 0.6.2-1 [89.5 kB] Get:26 http://ftpmaster.internal/ubuntu/ oneiric/main libunistring0 armel 0.9.3-4 [394 kB] Get:27 http://ftpmaster.internal/ubuntu/ oneiric/main gettext armel 0.18.1.1-3ubuntu1 [1156 kB] Get:28 http://ftpmaster.internal/ubuntu/ oneiric/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:29 http://ftpmaster.internal/ubuntu/ oneiric/main po-debconf all 1.0.16+nmu1 [212 kB] Get:30 http://ftpmaster.internal/ubuntu/ oneiric/main debhelper all 8.9.0ubuntu1 [487 kB] Get:31 http://ftpmaster.internal/ubuntu/ oneiric/main docbook-xsl all 1.75.2+dfsg-5ubuntu1 [1499 kB] Get:32 http://ftpmaster.internal/ubuntu/ oneiric/main gfortran-4.6 armel 4.6.1-7ubuntu2 [4614 kB] Get:33 http://ftpmaster.internal/ubuntu/ oneiric/main gfortran armel 4:4.6.1-2ubuntu5 [1210 B] Get:34 http://ftpmaster.internal/ubuntu/ oneiric/main libblas3gf armel 1.2.20110419-2 [187 kB] Get:35 http://ftpmaster.internal/ubuntu/ oneiric/main libexpat1-dev armel 2.0.1-7ubuntu3 [186 kB] Get:36 http://ftpmaster.internal/ubuntu/ oneiric/main liblapack3gf armel 3.3.0-4 [1755 kB] Get:37 http://ftpmaster.internal/ubuntu/ oneiric/main libopenbabel4 armel 2.3.0+dfsg-2ubuntu1 [3065 kB] Get:38 http://ftpmaster.internal/ubuntu/ oneiric/main libpython2.7 armel 2.7.2-5 [1002 kB] Get:39 http://ftpmaster.internal/ubuntu/ oneiric/main zlib1g-dev armel 1:1.2.3.4.dfsg-3ubuntu3 [161 kB] Get:40 http://ftpmaster.internal/ubuntu/ oneiric/main libssl-dev armel 1.0.0d-2ubuntu2 [1219 kB] Get:41 http://ftpmaster.internal/ubuntu/ oneiric/main libtool armel 2.4-2ubuntu1 [301 kB] Get:42 http://ftpmaster.internal/ubuntu/ oneiric/main libxml2-utils armel 2.7.8.dfsg-4 [37.3 kB] Get:43 http://ftpmaster.internal/ubuntu/ oneiric/main libxslt1.1 armel 1.1.26-7 [143 kB] Get:44 http://ftpmaster.internal/ubuntu/ oneiric/universe openbabel armel 2.3.0+dfsg-2ubuntu1 [112 kB] Get:45 http://ftpmaster.internal/ubuntu/ oneiric/main python2.7-dev armel 2.7.2-5 [4504 kB] Get:46 http://ftpmaster.internal/ubuntu/ oneiric/main python-dev all 2.7.2-5ubuntu1 [1000 B] Get:47 http://ftpmaster.internal/ubuntu/ oneiric/main python-support all 1.0.13ubuntu1 [26.6 kB] Get:48 http://ftpmaster.internal/ubuntu/ oneiric/main python-numpy armel 1:1.5.1-2ubuntu2 [1933 kB] Get:49 http://ftpmaster.internal/ubuntu/ oneiric/main swig armel 2.0.4+really1.3.40-3ubuntu4 [965 kB] Get:50 http://ftpmaster.internal/ubuntu/ oneiric/main xsltproc armel 1.1.26-7 [14.3 kB] Get:51 http://ftpmaster.internal/ubuntu/ oneiric/main xmlto armel 0.0.23-2 [33.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 32.8 MB in 10s (2995 kB/s) Selecting previously deselected package libdb4.8. (Reading database ... 13965 files and directories currently installed.) Unpacking libdb4.8 (from .../libdb4.8_4.8.30-9_armel.deb) ... Selecting previously deselected package libexpat1. Unpacking libexpat1 (from .../libexpat1_2.0.1-7ubuntu3_armel.deb) ... Selecting previously deselected package libsqlite3-0. Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.7-2ubuntu1_armel.deb) ... Selecting previously deselected package libpipeline1. Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_armel.deb) ... Selecting previously deselected package sgml-base. Unpacking sgml-base (from .../sgml-base_1.26+nmu1ubuntu1_all.deb) ... Selecting previously deselected package xml-core. Unpacking xml-core (from .../archives/xml-core_0.13_all.deb) ... Selecting previously deselected package sgml-data. Unpacking sgml-data (from .../sgml-data_2.0.6_all.deb) ... Setting up sgml-base (1.26+nmu1ubuntu1) ... Setting up xml-core (0.13) ... Selecting previously deselected package docbook-xml. (Reading database ... 14224 files and directories currently installed.) Unpacking docbook-xml (from .../docbook-xml_4.5-7_all.deb) ... Selecting previously deselected package libgfortran3. Unpacking libgfortran3 (from .../libgfortran3_4.6.1-7ubuntu2_armel.deb) ... Selecting previously deselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.04-5ubuntu3_armel.deb) ... Selecting previously deselected package file. Unpacking file (from .../file_5.04-5ubuntu3_armel.deb) ... Selecting previously deselected package mime-support. Unpacking mime-support (from .../mime-support_3.51-1ubuntu1_all.deb) ... Selecting previously deselected package python2.7. Unpacking python2.7 (from .../python2.7_2.7.2-5_armel.deb) ... Selecting previously deselected package python. Unpacking python (from .../python_2.7.2-5ubuntu1_all.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_armel.deb) ... Selecting previously deselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-3ubuntu1_armel.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_armel.deb) ... Selecting previously deselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_armel.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-2_armel.deb) ... Selecting previously deselected package m4. Unpacking m4 (from .../archives/m4_1.4.16-1_armel.deb) ... Selecting previously deselected package autoconf. Unpacking autoconf (from .../autoconf_2.68-1ubuntu1_all.deb) ... Selecting previously deselected package autotools-dev. Unpacking autotools-dev (from .../autotools-dev_20110511.1_all.deb) ... Selecting previously deselected package automake. Unpacking automake (from .../automake_1%3a1.11.1-1ubuntu1_all.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ... Selecting previously deselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-1_armel.deb) ... Selecting previously deselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-4_armel.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-3ubuntu1_armel.deb) ... Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_8.9.0ubuntu1_all.deb) ... Selecting previously deselected package docbook-xsl. Unpacking docbook-xsl (from .../docbook-xsl_1.75.2+dfsg-5ubuntu1_all.deb) ... Selecting previously deselected package gfortran-4.6. Unpacking gfortran-4.6 (from .../gfortran-4.6_4.6.1-7ubuntu2_armel.deb) ... Selecting previously deselected package gfortran. Unpacking gfortran (from .../gfortran_4%3a4.6.1-2ubuntu5_armel.deb) ... Selecting previously deselected package libblas3gf. Unpacking libblas3gf (from .../libblas3gf_1.2.20110419-2_armel.deb) ... Selecting previously deselected package libexpat1-dev. Unpacking libexpat1-dev (from .../libexpat1-dev_2.0.1-7ubuntu3_armel.deb) ... Selecting previously deselected package liblapack3gf. Unpacking liblapack3gf (from .../liblapack3gf_3.3.0-4_armel.deb) ... Selecting previously deselected package libopenbabel4. Unpacking libopenbabel4 (from .../libopenbabel4_2.3.0+dfsg-2ubuntu1_armel.deb) ... Selecting previously deselected package libpython2.7. Unpacking libpython2.7 (from .../libpython2.7_2.7.2-5_armel.deb) ... Selecting previously deselected package zlib1g-dev. Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3ubuntu3_armel.deb) ... Selecting previously deselected package libssl-dev. Unpacking libssl-dev (from .../libssl-dev_1.0.0d-2ubuntu2_armel.deb) ... Selecting previously deselected package libtool. Unpacking libtool (from .../libtool_2.4-2ubuntu1_armel.deb) ... Selecting previously deselected package libxml2-utils. Unpacking libxml2-utils (from .../libxml2-utils_2.7.8.dfsg-4_armel.deb) ... Selecting previously deselected package libxslt1.1. Unpacking libxslt1.1 (from .../libxslt1.1_1.1.26-7_armel.deb) ... Selecting previously deselected package openbabel. Unpacking openbabel (from .../openbabel_2.3.0+dfsg-2ubuntu1_armel.deb) ... Selecting previously deselected package python2.7-dev. Unpacking python2.7-dev (from .../python2.7-dev_2.7.2-5_armel.deb) ... Selecting previously deselected package python-dev. Unpacking python-dev (from .../python-dev_2.7.2-5ubuntu1_all.deb) ... Selecting previously deselected package python-support. Unpacking python-support (from .../python-support_1.0.13ubuntu1_all.deb) ... Selecting previously deselected package python-numpy. Unpacking python-numpy (from .../python-numpy_1%3a1.5.1-2ubuntu2_armel.deb) ... Selecting previously deselected package swig. Unpacking swig (from .../swig_2.0.4+really1.3.40-3ubuntu4_armel.deb) ... Selecting previously deselected package xsltproc. Unpacking xsltproc (from .../xsltproc_1.1.26-7_armel.deb) ... Selecting previously deselected package xmlto. Unpacking xmlto (from .../xmlto_0.0.23-2_armel.deb) ... Setting up libdb4.8 (4.8.30-9) ... Setting up libexpat1 (2.0.1-7ubuntu3) ... Setting up libsqlite3-0 (3.7.7-2ubuntu1) ... Setting up libpipeline1 (1.2.0-3) ... Setting up sgml-data (2.0.6) ... Setting up docbook-xml (4.5-7) ... Setting up libgfortran3 (4.6.1-7ubuntu2) ... Setting up libmagic1 (5.04-5ubuntu3) ... Setting up file (5.04-5ubuntu3) ... Setting up mime-support (3.51-1ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode. Setting up python2.7 (2.7.2-5) ... Setting up python (2.7.2-5ubuntu1) ... Setting up bsdmainutils (8.2.3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up gettext-base (0.18.1.1-3ubuntu1) ... Setting up groff-base (1.21-6) ... Setting up libxml2 (2.7.8.dfsg-4) ... Setting up man-db (2.6.0.2-2) ... Building database of manual pages ... Setting up m4 (1.4.16-1) ... Setting up autoconf (2.68-1ubuntu1) ... Setting up autotools-dev (20110511.1) ... Setting up automake (1:1.11.1-1ubuntu1) ... update-alternatives: using /usr/bin/automake-1.11 to provide /usr/bin/automake (automake) in auto mode. Setting up html2text (1.3.2a-15) ... Setting up libcroco3 (0.6.2-1) ... Setting up libunistring0 (0.9.3-4) ... Setting up gettext (0.18.1.1-3ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu1) ... Setting up debhelper (8.9.0ubuntu1) ... Setting up docbook-xsl (1.75.2+dfsg-5ubuntu1) ... Setting up gfortran-4.6 (4.6.1-7ubuntu2) ... Setting up gfortran (4:4.6.1-2ubuntu5) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode. Setting up libblas3gf (1.2.20110419-2) ... update-alternatives: using /usr/lib/libblas/libblas.so.3gf to provide /usr/lib/libblas.so.3gf (libblas.so.3gf) in auto mode. Setting up libexpat1-dev (2.0.1-7ubuntu3) ... Setting up liblapack3gf (3.3.0-4) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3gf to provide /usr/lib/liblapack.so.3gf (liblapack.so.3gf) in auto mode. Setting up libopenbabel4 (2.3.0+dfsg-2ubuntu1) ... Setting up libpython2.7 (2.7.2-5) ... Setting up zlib1g-dev (1:1.2.3.4.dfsg-3ubuntu3) ... Setting up libssl-dev (1.0.0d-2ubuntu2) ... Setting up libtool (2.4-2ubuntu1) ... Setting up libxml2-utils (2.7.8.dfsg-4) ... Setting up libxslt1.1 (1.1.26-7) ... Setting up openbabel (2.3.0+dfsg-2ubuntu1) ... Setting up python2.7-dev (2.7.2-5) ... Setting up python-dev (2.7.2-5ubuntu1) ... Setting up python-support (1.0.13ubuntu1) ... Setting up python-numpy (1:1.5.1-2ubuntu2) ... Setting up swig (2.0.4+really1.3.40-3ubuntu4) ... Setting up xsltproc (1.1.26-7) ... Setting up xmlto (0.0.23-2) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Processing triggers for python-support ... Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.13-17ubuntu2 make_3.81-8.1ubuntu1 dpkg-dev_1.16.0.3ubuntu3 gcc-4.6_4.6.1-7ubuntu2 g++-4.6_4.6.1-7ubuntu2 binutils_2.21.53.20110810-0ubuntu1 libstdc++6-4.6-dev_4.6.1-7ubuntu2 libstdc++6_4.6.1-7ubuntu2 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Sun Jan 30 11:12:02 2011 UTC using DSA key ID CC8D7957 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./pdb2pqr_1.7-1.dsc dpkg-source: info: extracting pdb2pqr in pdb2pqr-1.7 dpkg-source: info: unpacking pdb2pqr_1.7.orig.tar.gz dpkg-source: info: unpacking pdb2pqr_1.7-1.debian.tar.gz dpkg-source: info: applying fix-includes.patch dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2 dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): -Wl,-Bsymbolic-functions dpkg-buildpackage: source package pdb2pqr dpkg-buildpackage: source version 1.7-1 dpkg-source --before-build pdb2pqr-1.7 dpkg-buildpackage: host architecture armel /usr/bin/fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean dh_clean debian/rules build dh build dh_testdir dh_auto_configure checking build system type... arm-unknown-linux-gnueabi checking host system type... arm-unknown-linux-gnueabi checking target system type... arm-unknown-linux-gnueabi 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-propka... no ------------- Begin Processing PropKa Configure Options ----------- checking build system type... armv7l-unknown-linux-gnueabi checking host system type... armv7l-unknown-linux-gnueabi checking target system type... armv7l-unknown-linux-gnueabi checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for python... /usr/bin/python checking for gcc... gcc checking for C compiler default output... 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 gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for g77... no checking for f77... no checking for xlf... no checking for frt... no checking for pgf77... no checking for fl32... no checking for af77... no checking for fort77... no checking for f90... no checking for xlf90... no checking for pgf90... no checking for epcf90... no checking for f95... f95 checking whether we are using the GNU Fortran 77 compiler... yes checking whether f95 accepts -g... yes checking how to run the C preprocessor... gcc -E checking for python include directory... -I/usr/include/python2.7 configure: creating ./config.status config.status: creating Makefile config.status: executing depfiles commands ------------- End Processing PropKa Configure Options ----------- 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 checking for numpy includes files... /usr/bin/python: can't open file './contrib/numpy-1.1.0/setup.py': [Errno 2] No such file or directory -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: 1.7 Install Dir: /usr/ propka: enable 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://buttercup/pdb2pqr/ (WEBSITE can be changed with the --with-url option) PDB2PQR_CGI (path to pdb2pqr.cgi): http://buttercup/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://buttercup/pdb2pqr/ after you run "make install" dh_auto_build make[1]: Entering directory `/build/buildd/pdb2pqr-1.7' cd . && : cd . && : --gnu Making all in propka make[2]: Entering directory `/build/buildd/pdb2pqr-1.7/propka' cd . && \ : --gnu Makefile gcc -DPACKAGE_NAME=\"PropKa\" -DPACKAGE_TARNAME=\"propka\" -DPACKAGE_VERSION=\"1.0.0\" -DPACKAGE_STRING=\"PropKa\ 1.0.0\" -DPACKAGE_BUGREPORT=\"Jan-Jensen@uiowa.edu\" -DPACKAGE=\"PropKa\" -DVERSION=\"1.0.0\" -I. -I. -I/usr/include/python2.7 -g -O2 -c `test -f 'propkalib.c' || echo './'`propkalib.c f95 -g -O2 -c -o propka.o `test -f 'propka.f' || echo './'`propka.f propka.f:90.34: CALL RUNPROPKA(NATOM, PDB, 'PROPKATMP3') 1 Warning: Character length of actual argument shorter than of dummy argument 'outname' (10/100) at (1) gcc -DPACKAGE_NAME=\"PropKa\" -DPACKAGE_TARNAME=\"propka\" -DPACKAGE_VERSION=\"1.0.0\" -DPACKAGE_STRING=\"PropKa\ 1.0.0\" -DPACKAGE_BUGREPORT=\"Jan-Jensen@uiowa.edu\" -DPACKAGE=\"PropKa\" -DVERSION=\"1.0.0\" -I. -I. -I/usr/include/python2.7 -g -O2 -c `test -f 'propkac.c' || echo './'`propkac.c f95 -o _propkalib.so -shared propkalib.o propka.o propkac.o /usr/bin/ld: propkalib.o: relocation R_ARM_THM_MOVW_ABS_NC against `a local symbol' can not be used when making a shared object; recompile with -fPIC propkalib.o: could not read symbols: Bad value collect2: ld returned 1 exit status make[2]: *** [_propkalib.so] Error 1 make[2]: Leaving directory `/build/buildd/pdb2pqr-1.7/propka' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/build/buildd/pdb2pqr-1.7' dh_auto_build: make -j1 returned exit code 2 make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ****************************************************************************** Build finished at 20110903-1329 FAILED [dpkg-buildpackage died] Purging chroot-autobuild/build/buildd/pdb2pqr-1.7 ------------------------------------------------------------------------------ /usr/bin/sudo dpkg --purge groff-base mime-support m4 gettext file zlib1g-dev sgml-data libxml2-utils autotools-dev po-debconf libdb4.8 python-numpy swig libcroco3 gfortran python-support libxml2 libopenbabel4 automake python-dev man-db libtool intltool-debian python2.7-dev python2.7 liblapack3gf libexpat1-dev libpython2.7 xml-core html2text gettext-base debhelper xmlto sgml-base libunistring0 python docbook-xml libxslt1.1 libblas3gf libmagic1 libpipeline1 libgfortran3 libexpat1 libsqlite3-0 libssl-dev bsdmainutils openbabel xsltproc gfortran-4.6 autoconf docbook-xsl (Reading database ... 18768 files and directories currently installed.) Removing python-numpy ... Removing swig ... Removing gfortran ... Removing python-support ... Purging configuration files for python-support ... Removing automake ... Removing python-dev ... Removing libtool ... Removing python2.7-dev ... Removing liblapack3gf ... Purging configuration files for liblapack3gf ... Removing libexpat1-dev ... Removing libpython2.7 ... Purging configuration files for libpython2.7 ... Removing debhelper ... Removing xmlto ... Removing python ... Purging configuration files for python ... Removing docbook-xml ... Purging configuration files for docbook-xml ... Removing libblas3gf ... Purging configuration files for libblas3gf ... Removing libssl-dev ... Removing openbabel ... Removing xsltproc ... Removing gfortran-4.6 ... Removing autoconf ... Purging configuration files for autoconf ... Removing docbook-xsl ... Purging configuration files for docbook-xsl ... Removing m4 ... Removing file ... Removing zlib1g-dev ... Removing sgml-data ... Purging configuration files for sgml-data ... Removing libxml2-utils ... Removing autotools-dev ... Removing po-debconf ... Removing libopenbabel4 ... Purging configuration files for libopenbabel4 ... Removing man-db ... Purging configuration files for man-db ... Removing catpages as well as /var/cache/man hierarchy. Removing intltool-debian ... Removing python2.7 ... Purging configuration files for python2.7 ... Removing xml-core ... Purging configuration files for xml-core ... dpkg: warning: while removing xml-core, directory '/etc/sgml' not empty so not removed. Removing html2text ... Purging configuration files for html2text ... Removing sgml-base ... Purging configuration files for sgml-base ... Removing libxslt1.1 ... Purging configuration files for libxslt1.1 ... Removing libmagic1 ... Purging configuration files for libmagic1 ... Removing libpipeline1 ... Purging configuration files for libpipeline1 ... Removing libgfortran3 ... Purging configuration files for libgfortran3 ... Removing libexpat1 ... Purging configuration files for libexpat1 ... Removing libsqlite3-0 ... Purging configuration files for libsqlite3-0 ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing groff-base ... Purging configuration files for groff-base ... Removing mime-support ... Purging configuration files for mime-support ... Removing gettext ... Removing libdb4.8 ... Removing libcroco3 ... Purging configuration files for libcroco3 ... Removing libxml2 ... Purging configuration files for libxml2 ... Removing gettext-base ... Removing libunistring0 ... Purging configuration files for libunistring0 ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place ****************************************************************************** Finished at 20110903-1331 Build needed 00:02:37, 9964k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', 'ccc6d0ce9756546b6d2bdf229438d70f02628f08'] Scanning for processes to kill in build /home/buildd/build-ccc6d0ce9756546b6d2bdf229438d70f02628f08/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'ccc6d0ce9756546b6d2bdf229438d70f02628f08'] Unmounting chroot for build ccc6d0ce9756546b6d2bdf229438d70f02628f08... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'ccc6d0ce9756546b6d2bdf229438d70f02628f08'] Removing build ccc6d0ce9756546b6d2bdf229438d70f02628f08