DC-Build-Header: pymol 1.4.1-1 / Sun Sep 11 12:50:22 +0200 2011 sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on talc-101.nancy.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ pymol 1.4.1-1 (amd64) 11 Sep 2011 12:50 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: pymol Version: 1.4.1-1 Source Version: 1.4.1-1 Distribution: lsid64c Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Hit http://localhost sid Release.gpg Hit http://localhost sid Release Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Hit http://localhost sid/main Sources Hit http://localhost sid/main amd64 Packages Ign http://localhost sid/main Translation-en Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: binutils cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libc-bin libc-dev-bin libc6 libc6-dev libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev multiarch-support 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 34.4 MB of archives. After this operation, 1073 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libc6-dev libc-dev-bin libgomp1 gcc-4.6-base libgcc1 cpp-4.6 libquadmath0 libstdc++6-4.6-dev g++-4.6 gcc-4.6 libstdc++6 binutils libc-bin libc6 multiarch-support Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libc6-dev amd64 2.13-20 [2637 kB] Get:2 http://localhost/debian/ sid/main libc-dev-bin amd64 2.13-20 [217 kB] Get:3 http://localhost/debian/ sid/main libgomp1 amd64 4.6.1-10 [25.7 kB] Get:4 http://localhost/debian/ sid/main gcc-4.6-base amd64 4.6.1-10 [135 kB] Get:5 http://localhost/debian/ sid/main libgcc1 amd64 1:4.6.1-10 [42.9 kB] Get:6 http://localhost/debian/ sid/main cpp-4.6 amd64 4.6.1-10 [4816 kB] Get:7 http://localhost/debian/ sid/main libquadmath0 amd64 4.6.1-10 [126 kB] Get:8 http://localhost/debian/ sid/main libstdc++6-4.6-dev amd64 4.6.1-10 [1660 kB] Get:9 http://localhost/debian/ sid/main g++-4.6 amd64 4.6.1-10 [6952 kB] Get:10 http://localhost/debian/ sid/main gcc-4.6 amd64 4.6.1-10 [7303 kB] Get:11 http://localhost/debian/ sid/main libstdc++6 amd64 4.6.1-10 [337 kB] Get:12 http://localhost/debian/ sid/main binutils amd64 2.21.53.20110910-1 [4844 kB] Get:13 http://localhost/debian/ sid/main libc-bin amd64 2.13-20 [819 kB] Get:14 http://localhost/debian/ sid/main libc6 amd64 2.13-20 [4323 kB] Get:15 http://localhost/debian/ sid/main multiarch-support amd64 2.13-20 [141 kB] Preconfiguring packages ... Fetched 34.4 MB in 0s (63.0 MB/s) (Reading database ... 10788 files and directories currently installed.) Preparing to replace libc6-dev 2.13-18 (using .../libc6-dev_2.13-20_amd64.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-dev-bin 2.13-18 (using .../libc-dev-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libgomp1 4.6.1-9 (using .../libgomp1_4.6.1-10_amd64.deb) ... Unpacking replacement libgomp1 ... Preparing to replace gcc-4.6-base 4.6.1-9 (using .../gcc-4.6-base_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6-base ... Setting up gcc-4.6-base (4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace libgcc1 1:4.6.1-9 (using .../libgcc1_1%3a4.6.1-10_amd64.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace cpp-4.6 4.6.1-9 (using .../cpp-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement cpp-4.6 ... Preparing to replace libquadmath0 4.6.1-9 (using .../libquadmath0_4.6.1-10_amd64.deb) ... Unpacking replacement libquadmath0 ... Preparing to replace libstdc++6-4.6-dev 4.6.1-9 (using .../libstdc++6-4.6-dev_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6-4.6-dev ... Preparing to replace g++-4.6 4.6.1-9 (using .../g++-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement g++-4.6 ... Preparing to replace gcc-4.6 4.6.1-9 (using .../gcc-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6 ... Preparing to replace libstdc++6 4.6.1-9 (using .../libstdc++6_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.6.1-10) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace binutils 2.21.53.20110823-3 (using .../binutils_2.21.53.20110910-1_amd64.deb) ... Unpacking replacement binutils ... Preparing to replace libc-bin 2.13-18 (using .../libc-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace libc6 2.13-18 (using .../libc6_2.13-20_amd64.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace multiarch-support 2.13-18 (using .../multiarch-support_2.13-20_amd64.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.13-20) ... Setting up libc-dev-bin (2.13-20) ... Setting up libc6-dev (2.13-20) ... Setting up libgomp1 (4.6.1-10) ... Setting up cpp-4.6 (4.6.1-10) ... Setting up libquadmath0 (4.6.1-10) ... Setting up binutils (2.21.53.20110910-1) ... Setting up gcc-4.6 (4.6.1-10) ... Setting up libstdc++6-4.6-dev (4.6.1-10) ... Setting up g++-4.6 (4.6.1-10) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'pymol' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debichem/unstable/pymol/ Need to get 10.9 MB of source archives. Get:1 http://localhost/debian/ sid/main pymol 1.4.1-1 (dsc) [1372 B] Get:2 http://localhost/debian/ sid/main pymol 1.4.1-1 (tar) [10.8 MB] Get:3 http://localhost/debian/ sid/main pymol 1.4.1-1 (diff) [53.6 kB] Fetched 10.9 MB in 1s (10.5 MB/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 `/build/pymol-LBsBoe/resolver-zmYuG9/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/698 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Selecting previously deselected package sbuild-build-depends-core-dummy. (Reading database ... 10801 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Cannot open /var/lib/schroot/mount/lsid64c-03eb60df-8512-4dfd-98d5-b65eb19715ab/etc/lsb-release: No such file or directory Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 5), dpatch, python, python-dev, python-numpy, freeglut3-dev, libglew1.5-dev, libpng12-0-dev, tk8.4-dev, libfreetype6-dev, python-support (>= 0.4), texlive-latex-base Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 5), dpatch, python, python-dev, python-numpy, freeglut3-dev, libglew1.5-dev, libpng12-0-dev, tk8.4-dev, libfreetype6-dev, python-support (>= 0.4), texlive-latex-base dpkg-deb: building package `sbuild-build-depends-pymol-dummy' in `/build/pymol-LBsBoe/resolver-xNXmzf/apt_archive/sbuild-build-depends-pymol-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install pymol build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils debhelper dpatch ed file fontconfig-config freeglut3 freeglut3-dev gettext gettext-base groff-base html2text intltool-debian libblas3gf libcroco3 libdb4.8 libdrm2 libexpat1 libfontconfig1 libfreetype6 libfreetype6-dev libgfortran3 libgl1-mesa-dev libgl1-mesa-glx libglapi-mesa libglew1.6 libglew1.6-dev libglib2.0-0 libglu1-mesa libglu1-mesa-dev libice-dev libice6 libjpeg62 libkpathsea5 liblapack3gf liblcms1 libmagic1 libopenjpeg2 libpaper-utils libpaper1 libpcre3 libpipeline1 libpng12-0 libpng12-dev libpoppler13 libpthread-stubs0 libpthread-stubs0-dev libpython2.6 libsm-dev libsm6 libsqlite3-0 libssl-dev libssl1.0.0 libunistring0 libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxaw7 libxcb1 libxcb1-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxi6 libxml2 libxmu6 libxpm4 libxt-dev libxt6 libxxf86vm1 luatex man-db mesa-common-dev mime-support po-debconf python python-dev python-minimal python-numpy python-support python2.6 python2.6-dev python2.6-minimal tcl8.4 tcl8.4-dev tex-common texlive-base texlive-binaries texlive-common texlive-doc-base texlive-latex-base tk8.4 tk8.4-dev ttf-dejavu-core ucf x11-common x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-xext-dev xorg-sgml-doctools xtrans-dev zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make curl gettext-doc groff glew-utils liblcms-utils www-browser libmail-box-perl python-doc python-tk python-numpy-doc python-numpy-dbg python-nose gfortran python2.6-doc binfmt-support tclreadline tcl8.4-doc perl-tk ghostscript xpdf-reader pdf-viewer gv postscript-viewer tk8.4-doc Recommended packages: patchutils autopoint libgl1-mesa-dri libglib2.0-data shared-mime-info poppler-data libssl-doc xml-core texlive-luatex libmail-sendmail-perl lmodern texlive-latex-base-doc xterm x-terminal-emulator The following NEW packages will be installed: bsdmainutils debhelper dpatch ed file fontconfig-config freeglut3 freeglut3-dev gettext gettext-base groff-base html2text intltool-debian libblas3gf libcroco3 libdb4.8 libdrm2 libexpat1 libfontconfig1 libfreetype6 libfreetype6-dev libgfortran3 libgl1-mesa-dev libgl1-mesa-glx libglapi-mesa libglew1.6 libglew1.6-dev libglib2.0-0 libglu1-mesa libglu1-mesa-dev libice-dev libice6 libjpeg62 libkpathsea5 liblapack3gf liblcms1 libmagic1 libopenjpeg2 libpaper-utils libpaper1 libpcre3 libpipeline1 libpng12-0 libpng12-dev libpoppler13 libpthread-stubs0 libpthread-stubs0-dev libpython2.6 libsm-dev libsm6 libsqlite3-0 libssl-dev libssl1.0.0 libunistring0 libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxaw7 libxcb1 libxcb1-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxi6 libxml2 libxmu6 libxpm4 libxt-dev libxt6 libxxf86vm1 luatex man-db mesa-common-dev mime-support po-debconf python python-dev python-minimal python-numpy python-support python2.6 python2.6-dev python2.6-minimal sbuild-build-depends-pymol-dummy tcl8.4 tcl8.4-dev tex-common texlive-base texlive-binaries texlive-common texlive-doc-base texlive-latex-base tk8.4 tk8.4-dev ttf-dejavu-core ucf x11-common x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-xext-dev xorg-sgml-doctools xtrans-dev zlib1g-dev 0 upgraded, 109 newly installed, 0 to remove and 0 not upgraded. Need to get 79.0 MB/79.0 MB of archives. After this operation, 225 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libssl1.0.0 libpcre3 libdrm2 libexpat1 libfreetype6 ucf ttf-dejavu-core fontconfig-config libfontconfig1 libgfortran3 libglapi-mesa libxau6 libxdmcp6 libxcb1 libx11-data libx11-6 libxfixes3 libxdamage1 libxext6 libxxf86vm1 libgl1-mesa-glx libglu1-mesa libxi6 x11-common libice6 libsm6 libxt6 libxmu6 libglew1.6 libpng12-0 libdb4.8 bsdmainutils groff-base man-db libmagic1 file gettext-base libsqlite3-0 libxml2 mime-support python2.6-minimal python2.6 python-minimal python python-support html2text libglib2.0-0 libcroco3 libunistring0 gettext intltool-debian po-debconf debhelper dpatch ed freeglut3 xorg-sgml-doctools x11proto-core-dev libxau-dev libxdmcp-dev x11proto-input-dev x11proto-kb-dev xtrans-dev libpthread-stubs0 libpthread-stubs0-dev libxcb1-dev libx11-dev mesa-common-dev x11proto-xext-dev libxext-dev libgl1-mesa-dev libglu1-mesa-dev libice-dev libsm-dev libxt-dev freeglut3-dev libblas3gf zlib1g-dev libfreetype6-dev libglew1.6-dev libjpeg62 libkpathsea5 liblapack3gf liblcms1 libopenjpeg2 libpaper1 libpaper-utils libpng12-dev libpoppler13 libpython2.6 libssl-dev libxpm4 libxaw7 luatex python2.6-dev python-dev python-numpy tcl8.4 tcl8.4-dev tex-common texlive-common texlive-doc-base texlive-binaries texlive-base texlive-latex-base tk8.4 tk8.4-dev sbuild-build-depends-pymol-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-3 [37.9 kB] Get:2 http://localhost/debian/ sid/main libssl1.0.0 amd64 1.0.0e-2 [1143 kB] Get:3 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:4 http://localhost/debian/ sid/main libdrm2 amd64 2.4.26-1 [428 kB] Get:5 http://localhost/debian/ sid/main libexpat1 amd64 2.0.1-7 [137 kB] Get:6 http://localhost/debian/ sid/main libfreetype6 amd64 2.4.6-2 [435 kB] Get:7 http://localhost/debian/ sid/main ucf all 3.0025+nmu2 [70.6 kB] Get:8 http://localhost/debian/ sid/main ttf-dejavu-core all 2.33-2 [1552 kB] Get:9 http://localhost/debian/ sid/main fontconfig-config all 2.8.0-3 [221 kB] Get:10 http://localhost/debian/ sid/main libfontconfig1 amd64 2.8.0-3 [282 kB] Get:11 http://localhost/debian/ sid/main libgfortran3 amd64 4.6.1-10 [358 kB] Get:12 http://localhost/debian/ sid/main libglapi-mesa amd64 7.11-5 [55.1 kB] Get:13 http://localhost/debian/ sid/main libxau6 amd64 1:1.0.6-3 [17.0 kB] Get:14 http://localhost/debian/ sid/main libxdmcp6 amd64 1:1.1.0-3 [22.9 kB] Get:15 http://localhost/debian/ sid/main libxcb1 amd64 1.7-3 [45.4 kB] Get:16 http://localhost/debian/ sid/main libx11-data all 2:1.4.4-1 [183 kB] Get:17 http://localhost/debian/ sid/main libx11-6 amd64 2:1.4.4-1 [889 kB] Get:18 http://localhost/debian/ sid/main libxfixes3 amd64 1:5.0-4 [21.5 kB] Get:19 http://localhost/debian/ sid/main libxdamage1 amd64 1:1.1.3-2 [14.3 kB] Get:20 http://localhost/debian/ sid/main libxext6 amd64 2:1.3.0-3 [52.3 kB] Get:21 http://localhost/debian/ sid/main libxxf86vm1 amd64 1:1.1.1-2 [18.2 kB] Get:22 http://localhost/debian/ sid/main libgl1-mesa-glx amd64 7.11-5 [155 kB] Get:23 http://localhost/debian/ sid/main libglu1-mesa amd64 7.11-5 [220 kB] Get:24 http://localhost/debian/ sid/main libxi6 amd64 2:1.4.3-3 [66.2 kB] Get:25 http://localhost/debian/ sid/main x11-common all 1:7.6+8 [276 kB] Get:26 http://localhost/debian/ sid/main libice6 amd64 2:1.0.7-2 [56.5 kB] Get:27 http://localhost/debian/ sid/main libsm6 amd64 2:1.2.0-2 [29.8 kB] Get:28 http://localhost/debian/ sid/main libxt6 amd64 1:1.1.1-2 [207 kB] Get:29 http://localhost/debian/ sid/main libxmu6 amd64 2:1.1.0-2 [63.5 kB] Get:30 http://localhost/debian/ sid/main libglew1.6 amd64 1.6.0-4 [124 kB] Get:31 http://localhost/debian/ sid/main libpng12-0 amd64 1.2.46-3 [188 kB] Get:32 http://localhost/debian/ sid/main libdb4.8 amd64 4.8.30-9 [694 kB] Get:33 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:34 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:35 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-2 [1023 kB] Get:36 http://localhost/debian/ sid/main libmagic1 amd64 5.08-1 [246 kB] Get:37 http://localhost/debian/ sid/main file amd64 5.08-1 [51.7 kB] Get:38 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-4 [154 kB] Get:39 http://localhost/debian/ sid/main libsqlite3-0 amd64 3.7.7-2 [420 kB] Get:40 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-4 [892 kB] Get:41 http://localhost/debian/ sid/main mime-support all 3.51-1 [35.0 kB] Get:42 http://localhost/debian/ sid/main python2.6-minimal amd64 2.6.7-4 [1524 kB] Get:43 http://localhost/debian/ sid/main python2.6 amd64 2.6.7-4 [2483 kB] Get:44 http://localhost/debian/ sid/main python-minimal all 2.6.7-3 [39.2 kB] Get:45 http://localhost/debian/ sid/main python all 2.6.7-3 [177 kB] Get:46 http://localhost/debian/ sid/main python-support all 1.0.14 [33.5 kB] Get:47 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:48 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.28.6-1 [1648 kB] Get:49 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-1 [125 kB] Get:50 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-4 [437 kB] Get:51 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-4 [2079 kB] Get:52 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:53 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu1 [223 kB] Get:54 http://localhost/debian/ sid/main debhelper all 8.9.6 [562 kB] Get:55 http://localhost/debian/ sid/main dpatch all 2.0.32 [94.8 kB] Get:56 http://localhost/debian/ sid/main ed amd64 1.5-3 [63.1 kB] Get:57 http://localhost/debian/ sid/main freeglut3 amd64 2.6.0-1 [140 kB] Get:58 http://localhost/debian/ sid/main xorg-sgml-doctools all 1:1.8-2 [20.0 kB] Get:59 http://localhost/debian/ sid/main x11proto-core-dev all 7.0.22-1 [323 kB] Get:60 http://localhost/debian/ sid/main libxau-dev amd64 1:1.0.6-3 [20.5 kB] Get:61 http://localhost/debian/ sid/main libxdmcp-dev amd64 1:1.1.0-3 [56.5 kB] Get:62 http://localhost/debian/ sid/main x11proto-input-dev all 2.0.2-2 [82.3 kB] Get:63 http://localhost/debian/ sid/main x11proto-kb-dev all 1.0.5-2 [27.5 kB] Get:64 http://localhost/debian/ sid/main xtrans-dev all 1.2.6-2 [101 kB] Get:65 http://localhost/debian/ sid/main libpthread-stubs0 amd64 0.3-2.1 [3232 B] Get:66 http://localhost/debian/ sid/main libpthread-stubs0-dev amd64 0.3-2.1 [3554 B] Get:67 http://localhost/debian/ sid/main libxcb1-dev amd64 1.7-3 [83.1 kB] Get:68 http://localhost/debian/ sid/main libx11-dev amd64 2:1.4.4-1 [3383 kB] Get:69 http://localhost/debian/ sid/main mesa-common-dev amd64 7.11-5 [342 kB] Get:70 http://localhost/debian/ sid/main x11proto-xext-dev all 7.2.0-3 [255 kB] Get:71 http://localhost/debian/ sid/main libxext-dev amd64 2:1.3.0-3 [167 kB] Get:72 http://localhost/debian/ sid/main libgl1-mesa-dev amd64 7.11-5 [31.1 kB] Get:73 http://localhost/debian/ sid/main libglu1-mesa-dev amd64 7.11-5 [295 kB] Get:74 http://localhost/debian/ sid/main libice-dev amd64 2:1.0.7-2 [143 kB] Get:75 http://localhost/debian/ sid/main libsm-dev amd64 2:1.2.0-2 [101 kB] Get:76 http://localhost/debian/ sid/main libxt-dev amd64 1:1.1.1-2 [512 kB] Get:77 http://localhost/debian/ sid/main freeglut3-dev amd64 2.6.0-1 [215 kB] Get:78 http://localhost/debian/ sid/main libblas3gf amd64 1.2.20110419-2 [292 kB] Get:79 http://localhost/debian/ sid/main zlib1g-dev amd64 1:1.2.3.4.dfsg-3 [192 kB] Get:80 http://localhost/debian/ sid/main libfreetype6-dev amd64 2.4.6-2 [797 kB] Get:81 http://localhost/debian/ sid/main libglew1.6-dev amd64 1.6.0-4 [247 kB] Get:82 http://localhost/debian/ sid/main libjpeg62 amd64 6b1-2 [94.1 kB] Get:83 http://localhost/debian/ sid/main libkpathsea5 amd64 2009-11 [136 kB] Get:84 http://localhost/debian/ sid/main liblapack3gf amd64 3.3.1-1 [4437 kB] Get:85 http://localhost/debian/ sid/main liblcms1 amd64 1.19.dfsg-1 [111 kB] Get:86 http://localhost/debian/ sid/main libopenjpeg2 amd64 1.3+dfsg-4 [79.5 kB] Get:87 http://localhost/debian/ sid/main libpaper1 amd64 1.1.24+nmu1 [21.8 kB] Get:88 http://localhost/debian/ sid/main libpaper-utils amd64 1.1.24+nmu1 [18.1 kB] Get:89 http://localhost/debian/ sid/main libpng12-dev amd64 1.2.46-3 [265 kB] Get:90 http://localhost/debian/ sid/main libpoppler13 amd64 0.16.7-2 [1035 kB] Get:91 http://localhost/debian/ sid/main libpython2.6 amd64 2.6.7-4 [1087 kB] Get:92 http://localhost/debian/ sid/main libssl-dev amd64 1.0.0e-2 [1631 kB] Get:93 http://localhost/debian/ sid/main libxpm4 amd64 1:3.5.9-1 [48.4 kB] Get:94 http://localhost/debian/ sid/main libxaw7 amd64 2:1.0.9-2 [220 kB] Get:95 http://localhost/debian/ sid/main luatex amd64 0.70.1-1+b1 [2469 kB] Get:96 http://localhost/debian/ sid/main python2.6-dev amd64 2.6.7-4 [4832 kB] Get:97 http://localhost/debian/ sid/main python-dev all 2.6.7-3 [914 B] Get:98 http://localhost/debian/ sid/main python-numpy amd64 1:1.5.1-2+b1 [2171 kB] Get:99 http://localhost/debian/ sid/main tcl8.4 amd64 8.4.19-4 [1206 kB] Get:100 http://localhost/debian/ sid/main tcl8.4-dev amd64 8.4.19-4 [829 kB] Get:101 http://localhost/debian/ sid/main tex-common all 2.10 [725 kB] Get:102 http://localhost/debian/ sid/main texlive-common all 2009-13 [101 kB] Get:103 http://localhost/debian/ sid/main texlive-doc-base all 2009-2 [1345 kB] Get:104 http://localhost/debian/ sid/main texlive-binaries amd64 2009-11 [8069 kB] Get:105 http://localhost/debian/ sid/main texlive-base all 2009-13 [14.7 MB] Get:106 http://localhost/debian/ sid/main texlive-latex-base all 2009-13 [1423 kB] Get:107 http://localhost/debian/ sid/main tk8.4 amd64 8.4.19-4 [1053 kB] Get:108 http://localhost/debian/ sid/main tk8.4-dev amd64 8.4.19-4 [880 kB] Extracting templates from packages: 27% Extracting templates from packages: 55% Extracting templates from packages: 82% Extracting templates from packages: 100% Preconfiguring packages ... Fetched 79.0 MB in 1s (48.0 MB/s) Selecting previously deselected package libpipeline1. (Reading database ... 10801 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ... Selecting previously deselected package libssl1.0.0. Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-2_amd64.deb) ... Selecting previously deselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously deselected package libdrm2. Unpacking libdrm2 (from .../libdrm2_2.4.26-1_amd64.deb) ... Selecting previously deselected package libexpat1. Unpacking libexpat1 (from .../libexpat1_2.0.1-7_amd64.deb) ... Selecting previously deselected package libfreetype6. Unpacking libfreetype6 (from .../libfreetype6_2.4.6-2_amd64.deb) ... Selecting previously deselected package ucf. Unpacking ucf (from .../ucf_3.0025+nmu2_all.deb) ... Moving old data out of the way Selecting previously deselected package ttf-dejavu-core. 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Setting up ucf (3.0025+nmu2) ... Setting up ttf-dejavu-core (2.33-2) ... Setting up fontconfig-config (2.8.0-3) ... Setting up libfontconfig1 (2.8.0-3) ... Setting up libgfortran3 (4.6.1-10) ... Setting up libglapi-mesa (7.11-5) ... Setting up libxau6 (1:1.0.6-3) ... Setting up libxdmcp6 (1:1.1.0-3) ... Setting up libxcb1 (1.7-3) ... Setting up libx11-data (2:1.4.4-1) ... Setting up libx11-6 (2:1.4.4-1) ... Setting up libxfixes3 (1:5.0-4) ... Setting up libxdamage1 (1:1.1.3-2) ... Setting up libxext6 (2:1.3.0-3) ... Setting up libxxf86vm1 (1:1.1.1-2) ... Setting up libgl1-mesa-glx (7.11-5) ... Setting up libglu1-mesa (7.11-5) ... Setting up libxi6 (2:1.4.3-3) ... Setting up x11-common (1:7.6+8) ... invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6 (2:1.0.7-2) ... Setting up libsm6 (2:1.2.0-2) ... Setting up libxt6 (1:1.1.1-2) ... Setting up libxmu6 (2:1.1.0-2) ... Setting up libglew1.6 (1.6.0-4) ... Setting up libpng12-0 (1.2.46-3) ... 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Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu1) ... Setting up debhelper (8.9.6) ... Setting up dpatch (2.0.32) ... Setting up ed (1.5-3) ... Setting up freeglut3 (2.6.0-1) ... Setting up xorg-sgml-doctools (1:1.8-2) ... Setting up x11proto-core-dev (7.0.22-1) ... Setting up libxau-dev (1:1.0.6-3) ... Setting up libxdmcp-dev (1:1.1.0-3) ... Setting up x11proto-input-dev (2.0.2-2) ... Setting up x11proto-kb-dev (1.0.5-2) ... Setting up xtrans-dev (1.2.6-2) ... Setting up libpthread-stubs0 (0.3-2.1) ... Setting up libpthread-stubs0-dev (0.3-2.1) ... Setting up libxcb1-dev (1.7-3) ... Setting up libx11-dev (2:1.4.4-1) ... Setting up mesa-common-dev (7.11-5) ... Setting up x11proto-xext-dev (7.2.0-3) ... Setting up libxext-dev (2:1.3.0-3) ... Setting up libgl1-mesa-dev (7.11-5) ... Setting up libglu1-mesa-dev (7.11-5) ... Setting up libice-dev (2:1.0.7-2) ... Setting up libsm-dev (2:1.2.0-2) ... Setting up libxt-dev (1:1.1.1-2) ... Setting up freeglut3-dev (2.6.0-1) ... 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 zlib1g-dev (1:1.2.3.4.dfsg-3) ... Setting up libfreetype6-dev (2.4.6-2) ... Setting up libglew1.6-dev (1.6.0-4) ... Setting up libjpeg62 (6b1-2) ... Setting up libkpathsea5 (2009-11) ... Setting up liblapack3gf (3.3.1-1) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3gf to provide /usr/lib/liblapack.so.3gf (liblapack.so.3gf) in auto mode. Setting up liblcms1 (1.19.dfsg-1) ... Setting up libopenjpeg2 (1.3+dfsg-4) ... Setting up libpaper1 (1.1.24+nmu1) ... Creating config file /etc/papersize with new version Setting up libpaper-utils (1.1.24+nmu1) ... Setting up libpng12-dev (1.2.46-3) ... Setting up libpoppler13 (0.16.7-2) ... Setting up libpython2.6 (2.6.7-4) ... Setting up libssl-dev (1.0.0e-2) ... Setting up libxpm4 (1:3.5.9-1) ... Setting up libxaw7 (2:1.0.9-2) ... Setting up luatex (0.70.1-1+b1) ... texlive-base is not ready, cannot create formats Setting up python2.6-dev (2.6.7-4) ... Setting up python-dev (2.6.7-3) ... Setting up python-numpy (1:1.5.1-2+b1) ... Setting up tcl8.4 (8.4.19-4) ... update-alternatives: using /usr/bin/tclsh8.4 to provide /usr/bin/tclsh (tclsh) in auto mode. Setting up tcl8.4-dev (8.4.19-4) ... Setting up tex-common (2.10) ... Creating config file /etc/texmf/texmf.d/05TeXMF.cnf with new version Creating config file /etc/texmf/texmf.d/15Plain.cnf with new version Creating config file /etc/texmf/texmf.d/45TeXinputs.cnf with new version Creating config file /etc/texmf/texmf.d/55Fonts.cnf with new version Creating config file /etc/texmf/texmf.d/65BibTeX.cnf with new version Creating config file /etc/texmf/texmf.d/75DviPS.cnf with new version Creating config file /etc/texmf/texmf.d/80DVIPDFMx.cnf with new version Creating config file /etc/texmf/texmf.d/85Misc.cnf with new version Creating config file /etc/texmf/texmf.d/90TeXDoc.cnf with new version Creating config file /etc/texmf/texmf.d/95NonPath.cnf with new version Creating config file /etc/texmf/updmap.d/00updmap.cfg with new version Creating config file /etc/texmf/texmf.cnf with new version Running mktexlsr. This may take some time... done. texlive-base is not ready, delaying updmap-sys call texlive-base is not ready, skipping fmtutil-sys --all call Setting up texlive-common (2009-13) ... Setting up texlive-doc-base (2009-2) ... Setting up texlive-binaries (2009-11) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode. update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode. Building format(s) --refresh. This may take some time... done. Setting up tk8.4 (8.4.19-4) ... update-alternatives: using /usr/bin/wish8.4 to provide /usr/bin/wish (wish) in auto mode. Setting up tk8.4-dev (8.4.19-4) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Setting up texlive-base (2009-13) ... Creating config file /etc/texmf/dvips/config/config.ps with new version Creating config file /etc/texmf/tex/generic/config/pdftexconfig.tex with new version Creating config file /etc/texmf/dvipdfmx/dvipdfmx.cfg with new version Creating config file /etc/texmf/xdvi/XDvi with new version Running mktexlsr. This may take some time... done. Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-base.cnf. This may take some time... done. Processing triggers for tex-common ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building e-tex based formats --byhyphen /var/lib/texmf/tex/generic/config/language.def. This may take some time... done. Setting up texlive-latex-base (2009-13) ... Running mktexlsr. This may take some time... done. Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-latex-base.cnf. This may take some time... done. Processing triggers for tex-common ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up sbuild-build-depends-pymol-dummy (0.invalid.0) ... Processing triggers for python-support ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-10 gcc-4.6_4.6.1-10 libc6-dev_2.13-20 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 linux-libc-dev_3.0.0-3 Package versions: apt_0.8.15.6 apt-utils_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 clang_2.9-11 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-10 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffutils_1:3.0-1 dpatch_2.0.32 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 ed_1.5-3 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig-config_2.8.0-3 freeglut3_2.6.0-1 freeglut3-dev_2.6.0-1 g++_4:4.6.1-2 g++-4.6_4.6.1-10 gcc_4:4.6.1-2 gcc-4.6_4.6.1-10 gcc-4.6-base_4.6.1-10 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblas3gf_1.2.20110419-2 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc6_2.13-20 libc6-dev_2.13-20 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb4.8_4.8.30-9 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libdrm2_2.4.26-1 libexpat1_2.0.1-7 libffi5_3.0.10~rc10-3 libfontconfig1_2.8.0-3 libfreetype6_2.4.6-2 libfreetype6-dev_2.4.6-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-10 libgdbm3_1.8.3-10 libgfortran3_4.6.1-10 libgl1-mesa-dev_7.11-5 libgl1-mesa-glx_7.11-5 libglapi-mesa_7.11-5 libglew1.6_1.6.0-4 libglew1.6-dev_1.6.0-4 libglib2.0-0_2.28.6-1 libglu1-mesa_7.11-5 libglu1-mesa-dev_7.11-5 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-10 libice-dev_2:1.0.7-2 libice6_2:1.0.7-2 libjpeg62_6b1-2 libkpathsea5_2009-11 liblapack3gf_3.3.1-1 liblcms1_1.19.dfsg-1 libllvm2.9_2.9+dfsg-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libopenjpeg2_1.3+dfsg-4 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpaper-utils_1.1.24+nmu1 libpaper1_1.1.24+nmu1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpng12-dev_1.2.46-3 libpoppler13_0.16.7-2 libpthread-stubs0_0.3-2.1 libpthread-stubs0-dev_0.3-2.1 libpython2.6_2.6.7-4 libquadmath0_4.6.1-10 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libsm-dev_2:1.2.0-2 libsm6_2:1.2.0-2 libsqlite3-0_3.7.7-2 libss2_1.42~WIP-2011-07-02-1 libssl-dev_1.0.0e-2 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libx11-6_2:1.4.4-1 libx11-data_2:1.4.4-1 libx11-dev_2:1.4.4-1 libxau-dev_1:1.0.6-3 libxau6_1:1.0.6-3 libxaw7_2:1.0.9-2 libxcb1_1.7-3 libxcb1-dev_1.7-3 libxdamage1_1:1.1.3-2 libxdmcp-dev_1:1.1.0-3 libxdmcp6_1:1.1.0-3 libxext-dev_2:1.3.0-3 libxext6_2:1.3.0-3 libxfixes3_1:5.0-4 libxi6_2:1.4.3-3 libxml2_2.7.8.dfsg-4 libxmu6_2:1.1.0-2 libxpm4_1:3.5.9-1 libxt-dev_1:1.1.1-2 libxt6_1:1.1.1-2 libxxf86vm1_1:1.1.1-2 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 luatex_0.70.1-1+b1 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mesa-common-dev_7.11-5 mime-support_3.51-1 mount_2.19.1-5 multiarch-support_2.13-20 ncurses-base_5.9-1 ncurses-bin_5.9-1 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 python_2.6.7-3 python-dev_2.6.7-3 python-minimal_2.6.7-3 python-numpy_1:1.5.1-2+b1 python-support_1.0.14 python2.6_2.6.7-4 python2.6-dev_2.6.7-4 python2.6-minimal_2.6.7-4 readline-common_6.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pymol-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tcl8.4_8.4.19-4 tcl8.4-dev_8.4.19-4 tex-common_2.10 texlive-base_2009-13 texlive-binaries_2009-11 texlive-common_2009-13 texlive-doc-base_2009-2 texlive-latex-base_2009-13 tk8.4_8.4.19-4 tk8.4-dev_8.4.19-4 ttf-dejavu-core_2.33-2 tzdata_2011i-2 ucf_3.0025+nmu2 util-linux_2.19.1-5 x11-common_1:7.6+8 x11proto-core-dev_7.0.22-1 x11proto-input-dev_2.0.2-2 x11proto-kb-dev_1.0.5-2 x11proto-xext-dev_7.2.0-3 xorg-sgml-doctools_1:1.8-2 xtrans-dev_1.2.6-2 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Sat Aug 27 19:40:12 2011 CEST using DSA key ID 9ED101BF gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./pymol_1.4.1-1.dsc dpkg-source: info: extracting pymol in pymol-1.4.1 dpkg-source: info: unpacking pymol_1.4.1.orig.tar.gz dpkg-source: info: applying pymol_1.4.1-1.diff.gz Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── 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): dpkg-buildpackage: source package pymol dpkg-buildpackage: source version 1.4.1-1 dpkg-source --before-build pymol-1.4.1 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dpatch deapply-all 24_autodock_plugin not applied to ./ . 23_bts576210_FTBFS_ia64 not applied to ./ . 22_fix_pymol_import not applied to ./ . 21_fix_png_batch_mode not applied to ./ . 20_output_license_terms not applied to ./ . 19_blosum_matrix_path not applied to ./ . 17_cmyk_png_data_path not applied to ./ . 13_activate_vmd_plugin not applied to ./ . 11_fix__cmd_import not applied to ./ . 09_chempy_data_path not applied to ./ . 05_examples_data_path not applied to ./ . 03_povray not applied to ./ . 02_test-suite not applied to ./ . rm -rf patch-stamp patch-stampT debian/patched dh_testdir dh_testroot [ ! -f Makefile ] || /usr/bin/make distclean python setup.py clean running clean After running: python setup.py install Please run, to complete the installation: python setup2.py install To uninstall PyMOL, run: python setup2.py uninstall rm -rf build test/tmp test/cmp dh_clean build-stamp install-stamp debian/pymol.launch \ debian/pymol-ref-card.* Rules.make test/pymol-test dpkg-source -b pymol-1.4.1 dpkg-source: warning: no source format specified in debian/source/format, see dpkg-source(1) dpkg-source: info: using source format `1.0' dpkg-source: info: building pymol using existing pymol_1.4.1.orig.tar.gz dpkg-source: info: building pymol in pymol_1.4.1-1.diff.gz dpkg-source: warning: executable mode 0755 of 'debian/patches/17_cmyk_png_data_path.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/22_fix_pymol_import.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/23_bts576210_FTBFS_ia64.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/13_activate_vmd_plugin.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/19_blosum_matrix_path.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/21_fix_png_batch_mode.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/03_povray.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/05_examples_data_path.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/24_autodock_plugin.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/02_test-suite.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/09_chempy_data_path.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/20_output_license_terms.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/11_fix__cmd_import.dpatch' will not be represented in diff dpkg-source: info: building pymol in pymol_1.4.1-1.dsc debian/rules build test -d debian/patched || install -d debian/patched dpatch apply-all applying patch 02_test-suite to ./ ... ok. applying patch 03_povray to ./ ... ok. applying patch 05_examples_data_path to ./ ... ok. applying patch 09_chempy_data_path to ./ ... ok. applying patch 11_fix__cmd_import to ./ ... ok. applying patch 13_activate_vmd_plugin to ./ ... ok. applying patch 17_cmyk_png_data_path to ./ ... ok. applying patch 19_blosum_matrix_path to ./ ... ok. applying patch 20_output_license_terms to ./ ... ok. applying patch 21_fix_png_batch_mode to ./ ... ok. applying patch 22_fix_pymol_import to ./ ... ok. applying patch 23_bts576210_FTBFS_ia64 to ./ ... ok. applying patch 24_autodock_plugin to ./ ... ok. dpatch cat-all >>patch-stampT mv -f patch-stampT patch-stamp dh_testdir python setup.py build running build running build_py creating build creating build/lib.linux-x86_64-2.6 creating build/lib.linux-x86_64-2.6/chempy copying modules/chempy/mol2.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/hetatm.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/pkl.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/mae.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/cpv.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/protein.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/solvate.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/mass.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/bonds.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/__init__.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/neighbor.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/cif.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/mmd.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/dictdb.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/cc1.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/water_amber.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/protein_amber.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/pdb.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/io.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/water_residues.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/cex.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/place.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/bond_amber.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/map.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/bond_mmff.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/brick.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/lst.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/protein_mmff.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/protein_residues.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/sdf.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/gms.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/protein_amber99.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/xyz.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/models.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/charge.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/mol.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/arc.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/gamess1.py -> build/lib.linux-x86_64-2.6/chempy creating build/lib.linux-x86_64-2.6/chempy/bmin copying modules/chempy/bmin/state.py -> build/lib.linux-x86_64-2.6/chempy/bmin copying modules/chempy/bmin/__init__.py -> build/lib.linux-x86_64-2.6/chempy/bmin copying modules/chempy/bmin/realtime.py -> build/lib.linux-x86_64-2.6/chempy/bmin copying modules/chempy/bmin/util.py -> build/lib.linux-x86_64-2.6/chempy/bmin copying modules/chempy/bmin/commands.py -> build/lib.linux-x86_64-2.6/chempy/bmin creating build/lib.linux-x86_64-2.6/chempy/champ copying modules/chempy/champ/formal_charges.py -> build/lib.linux-x86_64-2.6/chempy/champ copying modules/chempy/champ/__init__.py -> build/lib.linux-x86_64-2.6/chempy/champ copying modules/chempy/champ/amber99.py -> build/lib.linux-x86_64-2.6/chempy/champ copying modules/chempy/champ/assign.py -> build/lib.linux-x86_64-2.6/chempy/champ creating build/lib.linux-x86_64-2.6/chempy/fast copying modules/chempy/fast/__init__.py -> build/lib.linux-x86_64-2.6/chempy/fast creating build/lib.linux-x86_64-2.6/chempy/fragments copying modules/chempy/fragments/__init__.py -> build/lib.linux-x86_64-2.6/chempy/fragments creating build/lib.linux-x86_64-2.6/chempy/tinker copying modules/chempy/tinker/__init__.py -> build/lib.linux-x86_64-2.6/chempy/tinker copying modules/chempy/tinker/state.py -> build/lib.linux-x86_64-2.6/chempy/tinker copying modules/chempy/tinker/realtime.py -> build/lib.linux-x86_64-2.6/chempy/tinker copying modules/chempy/tinker/keyword.py -> build/lib.linux-x86_64-2.6/chempy/tinker copying modules/chempy/tinker/amber.py -> build/lib.linux-x86_64-2.6/chempy/tinker creating build/lib.linux-x86_64-2.6/pmg_tk copying modules/pmg_tk/Setting.py -> build/lib.linux-x86_64-2.6/pmg_tk copying modules/pmg_tk/SetEditor.py -> build/lib.linux-x86_64-2.6/pmg_tk copying modules/pmg_tk/__init__.py -> build/lib.linux-x86_64-2.6/pmg_tk copying modules/pmg_tk/PMGApp.py -> build/lib.linux-x86_64-2.6/pmg_tk copying modules/pmg_tk/Demo.py -> build/lib.linux-x86_64-2.6/pmg_tk copying modules/pmg_tk/ColorEditor.py -> build/lib.linux-x86_64-2.6/pmg_tk creating build/lib.linux-x86_64-2.6/pmg_tk/startup copying modules/pmg_tk/startup/autodock.py -> build/lib.linux-x86_64-2.6/pmg_tk/startup copying modules/pmg_tk/startup/remote_pdb_load.py -> build/lib.linux-x86_64-2.6/pmg_tk/startup copying modules/pmg_tk/startup/__init__.py -> build/lib.linux-x86_64-2.6/pmg_tk/startup copying modules/pmg_tk/startup/apbs_tools.py -> build/lib.linux-x86_64-2.6/pmg_tk/startup creating build/lib.linux-x86_64-2.6/pmg_tk/skins copying modules/pmg_tk/skins/__init__.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins creating build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/__init__.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/volume.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ColorRampModel.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ModalWindow.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ColorMap.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/builder.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/SimpleColorChooser.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/hist.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal creating build/lib.linux-x86_64-2.6/pmg_wx copying modules/pmg_wx/__init__.py -> build/lib.linux-x86_64-2.6/pmg_wx creating build/lib.linux-x86_64-2.6/pymol copying modules/pymol/__init__.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/exporting.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/fitting.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/importing.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/povray.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/shortcut.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/viewing.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/computing.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/menu.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/feedingback.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/colorramping.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/vfont.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/moving.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/headering.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/setting.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/invocation.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/externing.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/completing.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/locking.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/editing.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/movie.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/checking.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/experimenting.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/parsing.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/m4x.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/selector.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/xray.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/util.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/keywords.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/creating.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/commanding.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/cmd.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/cgo.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/rpc.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/selecting.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/callback.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/parser.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/controlling.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/keyboard.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/api.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/gui.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/constants.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/monitoring.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/internal.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/helping.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/xwin.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/wizarding.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/editor.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/preset.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/querying.py -> build/lib.linux-x86_64-2.6/pymol creating build/lib.linux-x86_64-2.6/pymol/contrib copying modules/pymol/contrib/__init__.py -> build/lib.linux-x86_64-2.6/pymol/contrib creating build/lib.linux-x86_64-2.6/pymol/opengl copying modules/pymol/opengl/__init__.py -> build/lib.linux-x86_64-2.6/pymol/opengl creating build/lib.linux-x86_64-2.6/pymol/opengl/gl copying modules/pymol/opengl/gl/__init__.py -> build/lib.linux-x86_64-2.6/pymol/opengl/gl copying modules/pymol/opengl/gl/glconst.py -> build/lib.linux-x86_64-2.6/pymol/opengl/gl creating build/lib.linux-x86_64-2.6/pymol/opengl/glu copying modules/pymol/opengl/glu/__init__.py -> build/lib.linux-x86_64-2.6/pymol/opengl/glu copying modules/pymol/opengl/glu/gluconst.py -> build/lib.linux-x86_64-2.6/pymol/opengl/glu creating build/lib.linux-x86_64-2.6/pymol/opengl/glut copying modules/pymol/opengl/glut/__init__.py -> build/lib.linux-x86_64-2.6/pymol/opengl/glut copying modules/pymol/opengl/glut/glutconst.py -> build/lib.linux-x86_64-2.6/pymol/opengl/glut creating build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/mutagenesis.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/demo.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/toggle.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/message.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/filter.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/density.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/distance.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/appearance.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/measurement.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/cleanup.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/__init__.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/dragging.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/sculpting.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/security.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/pseudoatom.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/annotation.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/fedora.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/pair_fit.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/stereodemo.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/charge.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/renaming.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/benchmark.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/box.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/label.py -> build/lib.linux-x86_64-2.6/pymol/wizard creating build/lib.linux-x86_64-2.6/web copying modules/web/__init__.py -> build/lib.linux-x86_64-2.6/web copying modules/web/pymolhttpd.py -> build/lib.linux-x86_64-2.6/web creating build/lib.linux-x86_64-2.6/web/examples copying modules/web/examples/__init__.py -> build/lib.linux-x86_64-2.6/web/examples copying modules/web/examples/justhttpd.py -> build/lib.linux-x86_64-2.6/web/examples package init file 'modules/web/javascript/__init__.py' not found (or not a regular file) package init file 'modules/web/javascript/__init__.py' not found (or not a regular file) running build_ext building 'pymol._cmd' extension creating build/temp.linux-x86_64-2.6 creating build/temp.linux-x86_64-2.6/modules creating build/temp.linux-x86_64-2.6/modules/cealign creating build/temp.linux-x86_64-2.6/modules/cealign/src creating build/temp.linux-x86_64-2.6/ov creating build/temp.linux-x86_64-2.6/ov/src creating build/temp.linux-x86_64-2.6/layer0 creating build/temp.linux-x86_64-2.6/layer1 creating build/temp.linux-x86_64-2.6/layer2 creating build/temp.linux-x86_64-2.6/layer3 creating build/temp.linux-x86_64-2.6/layer4 creating build/temp.linux-x86_64-2.6/layer5 creating build/temp.linux-x86_64-2.6/contrib creating build/temp.linux-x86_64-2.6/contrib/uiuc creating build/temp.linux-x86_64-2.6/contrib/uiuc/plugins creating build/temp.linux-x86_64-2.6/contrib/uiuc/plugins/molfile_plugin creating build/temp.linux-x86_64-2.6/contrib/uiuc/plugins/molfile_plugin/src gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_VMD_PLUGINS -DNO_MMLIBS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c modules/cealign/src/ccealignmodule.cpp -o build/temp.linux-x86_64-2.6/modules/cealign/src/ccealignmodule.o -ffast-math -funroll-loops -O3 In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:41: modules/cealign/src/tnt/tnt_array1d.h:238:28: warning: '&&' within '||' [-Wlogical-op-parentheses] if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) ~~~~~~~~~~~~~~~~~~~~~ ^ modules/cealign/src/tnt/tnt_array1d.h:238:28: note: place parentheses around the '&&' expression to silence this warning if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) ^ ( ) In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:48: modules/cealign/src/tnt/tnt_fortran_array1d.h:224:28: warning: '&&' within '||' [-Wlogical-op-parentheses] if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) ~~~~~~~~~~~~~~~~~~~~~ ^ modules/cealign/src/tnt/tnt_fortran_array1d.h:224:28: note: place parentheses around the '&&' expression to silence this warning if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) ^ ( ) In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:55: modules/cealign/src/tnt/tnt_sparse_matrix_csr.h:97:3: error: no matching constructor for initialization of 'Array1D' rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {} ^ ~~~~ In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:41: modules/cealign/src/tnt/tnt_array1d.h:63:11: note: candidate constructor not viable: no known conversion from 'const int *' to 'const int' for 2nd argument Array1D(int n, const T &a); ^ modules/cealign/src/tnt/tnt_array1d.h:64:11: note: candidate constructor not viable: 2nd argument ('const int *') would lose const qualifier Array1D(int n, T *a); ^ modules/cealign/src/tnt/tnt_array1d.h:61:11: note: candidate constructor not viable: requires 0 arguments, but 2 were provided Array1D(); ^ modules/cealign/src/tnt/tnt_array1d.h:62:11: note: candidate constructor not viable: requires 1 argument, but 2 were provided explicit Array1D(int n); ^ modules/cealign/src/tnt/tnt_array1d.h:65:14: note: candidate constructor not viable: requires 1 argument, but 2 were provided inline Array1D(const Array1D &A); ^ In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:55: modules/cealign/src/tnt/tnt_sparse_matrix_csr.h:97:18: error: no matching constructor for initialization of 'Array1D' rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {} ^ ~~~~~ In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:41: modules/cealign/src/tnt/tnt_array1d.h:63:11: note: candidate constructor not viable: no known conversion from 'const int *' to 'const int' for 2nd argument Array1D(int n, const T &a); ^ modules/cealign/src/tnt/tnt_array1d.h:64:11: note: candidate constructor not viable: 2nd argument ('const int *') would lose const qualifier Array1D(int n, T *a); ^ modules/cealign/src/tnt/tnt_array1d.h:61:11: note: candidate constructor not viable: requires 0 arguments, but 2 were provided Array1D(); ^ modules/cealign/src/tnt/tnt_array1d.h:62:11: note: candidate constructor not viable: requires 1 argument, but 2 were provided explicit Array1D(int n); ^ modules/cealign/src/tnt/tnt_array1d.h:65:14: note: candidate constructor not viable: requires 1 argument, but 2 were provided inline Array1D(const Array1D &A); ^ In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:57: In file included from layer0/os_python.h:30: In file included from /usr/include/python2.6/Python.h:8: /usr/include/python2.6/pyconfig.h:1031:9: warning: '_POSIX_C_SOURCE' macro redefined #define _POSIX_C_SOURCE 200112L ^ In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:40: In file included from modules/cealign/src/tnt/tnt_math_utils.h:5: In file included from /usr/include/c++/4.6/cmath:42: In file included from /usr/include/c++/4.6//x86_64-linux-gnu/bits/c++config.h:392: In file included from /usr/include/c++/4.6//x86_64-linux-gnu/bits/os_defines.h:40: /usr/include/features.h:163:10: note: previous definition is here # define _POSIX_C_SOURCE 200809L ^ In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:57: In file included from layer0/os_python.h:30: In file included from /usr/include/python2.6/Python.h:8: /usr/include/python2.6/pyconfig.h:1040:9: warning: '_XOPEN_SOURCE' macro redefined #define _XOPEN_SOURCE 600 ^ In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:40: In file included from modules/cealign/src/tnt/tnt_math_utils.h:5: In file included from /usr/include/c++/4.6/cmath:42: In file included from /usr/include/c++/4.6//x86_64-linux-gnu/bits/c++config.h:392: In file included from /usr/include/c++/4.6//x86_64-linux-gnu/bits/os_defines.h:40: /usr/include/features.h:165:10: note: previous definition is here # define _XOPEN_SOURCE 700 ^ 4 warnings and 2 errors generated. error: command 'gcc' failed with exit status 1 make: *** [build-stamp] Error 1 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20110911-1251 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64c-03eb60df-8512-4dfd-98d5-b65eb19715ab/build/pymol-LBsBoe Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 47364 Build-Time: 2 Distribution: lsid64c Fail-Stage: build Install-Time: 23 Job: pymol_1.4.1-1 Package: pymol Package-Time: 37 Source-Version: 1.4.1-1 Space: 47364 Status: attempted Version: 1.4.1-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20110911-1251 Build needed 00:00:37, 47364k disc space DC-Message: Failed, but took only 38.577066. Retrying, you never know. Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on talc-101.nancy.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ pymol 1.4.1-1 (amd64) 11 Sep 2011 13:12 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: pymol Version: 1.4.1-1 Source Version: 1.4.1-1 Distribution: lsid64c Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Hit http://localhost sid Release.gpg Hit http://localhost sid Release Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Hit http://localhost sid/main Sources Hit http://localhost sid/main amd64 Packages Ign http://localhost sid/main Translation-en Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: binutils cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libc-bin libc-dev-bin libc6 libc6-dev libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev multiarch-support 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 34.4 MB of archives. After this operation, 1073 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libc6-dev libc-dev-bin libgomp1 gcc-4.6-base libgcc1 cpp-4.6 libquadmath0 libstdc++6-4.6-dev g++-4.6 gcc-4.6 libstdc++6 binutils libc-bin libc6 multiarch-support Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libc6-dev amd64 2.13-20 [2637 kB] Get:2 http://localhost/debian/ sid/main libc-dev-bin amd64 2.13-20 [217 kB] Get:3 http://localhost/debian/ sid/main libgomp1 amd64 4.6.1-10 [25.7 kB] Get:4 http://localhost/debian/ sid/main gcc-4.6-base amd64 4.6.1-10 [135 kB] Get:5 http://localhost/debian/ sid/main libgcc1 amd64 1:4.6.1-10 [42.9 kB] Get:6 http://localhost/debian/ sid/main cpp-4.6 amd64 4.6.1-10 [4816 kB] Get:7 http://localhost/debian/ sid/main libquadmath0 amd64 4.6.1-10 [126 kB] Get:8 http://localhost/debian/ sid/main libstdc++6-4.6-dev amd64 4.6.1-10 [1660 kB] Get:9 http://localhost/debian/ sid/main g++-4.6 amd64 4.6.1-10 [6952 kB] Get:10 http://localhost/debian/ sid/main gcc-4.6 amd64 4.6.1-10 [7303 kB] Get:11 http://localhost/debian/ sid/main libstdc++6 amd64 4.6.1-10 [337 kB] Get:12 http://localhost/debian/ sid/main binutils amd64 2.21.53.20110910-1 [4844 kB] Get:13 http://localhost/debian/ sid/main libc-bin amd64 2.13-20 [819 kB] Get:14 http://localhost/debian/ sid/main libc6 amd64 2.13-20 [4323 kB] Get:15 http://localhost/debian/ sid/main multiarch-support amd64 2.13-20 [141 kB] Preconfiguring packages ... Fetched 34.4 MB in 0s (64.0 MB/s) (Reading database ... 10788 files and directories currently installed.) Preparing to replace libc6-dev 2.13-18 (using .../libc6-dev_2.13-20_amd64.deb) ... Unpacking replacement libc6-dev ... Preparing to replace libc-dev-bin 2.13-18 (using .../libc-dev-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-dev-bin ... Preparing to replace libgomp1 4.6.1-9 (using .../libgomp1_4.6.1-10_amd64.deb) ... Unpacking replacement libgomp1 ... Preparing to replace gcc-4.6-base 4.6.1-9 (using .../gcc-4.6-base_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6-base ... Setting up gcc-4.6-base (4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace libgcc1 1:4.6.1-9 (using .../libgcc1_1%3a4.6.1-10_amd64.deb) ... Unpacking replacement libgcc1 ... Setting up libgcc1 (1:4.6.1-10) ... (Reading database ... 10788 files and directories currently installed.) Preparing to replace cpp-4.6 4.6.1-9 (using .../cpp-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement cpp-4.6 ... Preparing to replace libquadmath0 4.6.1-9 (using .../libquadmath0_4.6.1-10_amd64.deb) ... Unpacking replacement libquadmath0 ... Preparing to replace libstdc++6-4.6-dev 4.6.1-9 (using .../libstdc++6-4.6-dev_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6-4.6-dev ... Preparing to replace g++-4.6 4.6.1-9 (using .../g++-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement g++-4.6 ... Preparing to replace gcc-4.6 4.6.1-9 (using .../gcc-4.6_4.6.1-10_amd64.deb) ... Unpacking replacement gcc-4.6 ... Preparing to replace libstdc++6 4.6.1-9 (using .../libstdc++6_4.6.1-10_amd64.deb) ... Unpacking replacement libstdc++6 ... Setting up libstdc++6 (4.6.1-10) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace binutils 2.21.53.20110823-3 (using .../binutils_2.21.53.20110910-1_amd64.deb) ... Unpacking replacement binutils ... Preparing to replace libc-bin 2.13-18 (using .../libc-bin_2.13-20_amd64.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace libc6 2.13-18 (using .../libc6_2.13-20_amd64.deb) ... Unpacking replacement libc6 ... Setting up libc6 (2.13-20) ... (Reading database ... 10801 files and directories currently installed.) Preparing to replace multiarch-support 2.13-18 (using .../multiarch-support_2.13-20_amd64.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.13-20) ... Setting up libc-dev-bin (2.13-20) ... Setting up libc6-dev (2.13-20) ... Setting up libgomp1 (4.6.1-10) ... Setting up cpp-4.6 (4.6.1-10) ... Setting up libquadmath0 (4.6.1-10) ... Setting up binutils (2.21.53.20110910-1) ... Setting up gcc-4.6 (4.6.1-10) ... Setting up libstdc++6-4.6-dev (4.6.1-10) ... Setting up g++-4.6 (4.6.1-10) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'pymol' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debichem/unstable/pymol/ Need to get 10.9 MB of source archives. Get:1 http://localhost/debian/ sid/main pymol 1.4.1-1 (dsc) [1372 B] Get:2 http://localhost/debian/ sid/main pymol 1.4.1-1 (tar) [10.8 MB] Get:3 http://localhost/debian/ sid/main pymol 1.4.1-1 (diff) [53.6 kB] Fetched 10.9 MB in 0s (62.3 MB/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 `/build/pymol-Z8VmKP/resolver-glSoJ_/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/702 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Selecting previously deselected package sbuild-build-depends-core-dummy. (Reading database ... 10801 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Cannot open /var/lib/schroot/mount/lsid64c-e268e09c-c30e-4a11-990b-eb263208303d/etc/lsb-release: No such file or directory Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 5), dpatch, python, python-dev, python-numpy, freeglut3-dev, libglew1.5-dev, libpng12-0-dev, tk8.4-dev, libfreetype6-dev, python-support (>= 0.4), texlive-latex-base Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 5), dpatch, python, python-dev, python-numpy, freeglut3-dev, libglew1.5-dev, libpng12-0-dev, tk8.4-dev, libfreetype6-dev, python-support (>= 0.4), texlive-latex-base dpkg-deb: building package `sbuild-build-depends-pymol-dummy' in `/build/pymol-Z8VmKP/resolver-D_kDEs/apt_archive/sbuild-build-depends-pymol-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install pymol build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils debhelper dpatch ed file fontconfig-config freeglut3 freeglut3-dev gettext gettext-base groff-base html2text intltool-debian libblas3gf libcroco3 libdb4.8 libdrm2 libexpat1 libfontconfig1 libfreetype6 libfreetype6-dev libgfortran3 libgl1-mesa-dev libgl1-mesa-glx libglapi-mesa libglew1.6 libglew1.6-dev libglib2.0-0 libglu1-mesa libglu1-mesa-dev libice-dev libice6 libjpeg62 libkpathsea5 liblapack3gf liblcms1 libmagic1 libopenjpeg2 libpaper-utils libpaper1 libpcre3 libpipeline1 libpng12-0 libpng12-dev libpoppler13 libpthread-stubs0 libpthread-stubs0-dev libpython2.6 libsm-dev libsm6 libsqlite3-0 libssl-dev libssl1.0.0 libunistring0 libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxaw7 libxcb1 libxcb1-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxi6 libxml2 libxmu6 libxpm4 libxt-dev libxt6 libxxf86vm1 luatex man-db mesa-common-dev mime-support po-debconf python python-dev python-minimal python-numpy python-support python2.6 python2.6-dev python2.6-minimal tcl8.4 tcl8.4-dev tex-common texlive-base texlive-binaries texlive-common texlive-doc-base texlive-latex-base tk8.4 tk8.4-dev ttf-dejavu-core ucf x11-common x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-xext-dev xorg-sgml-doctools xtrans-dev zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make curl gettext-doc groff glew-utils liblcms-utils www-browser libmail-box-perl python-doc python-tk python-numpy-doc python-numpy-dbg python-nose gfortran python2.6-doc binfmt-support tclreadline tcl8.4-doc perl-tk ghostscript xpdf-reader pdf-viewer gv postscript-viewer tk8.4-doc Recommended packages: patchutils autopoint libgl1-mesa-dri libglib2.0-data shared-mime-info poppler-data libssl-doc xml-core texlive-luatex libmail-sendmail-perl lmodern texlive-latex-base-doc xterm x-terminal-emulator The following NEW packages will be installed: bsdmainutils debhelper dpatch ed file fontconfig-config freeglut3 freeglut3-dev gettext gettext-base groff-base html2text intltool-debian libblas3gf libcroco3 libdb4.8 libdrm2 libexpat1 libfontconfig1 libfreetype6 libfreetype6-dev libgfortran3 libgl1-mesa-dev libgl1-mesa-glx libglapi-mesa libglew1.6 libglew1.6-dev libglib2.0-0 libglu1-mesa libglu1-mesa-dev libice-dev libice6 libjpeg62 libkpathsea5 liblapack3gf liblcms1 libmagic1 libopenjpeg2 libpaper-utils libpaper1 libpcre3 libpipeline1 libpng12-0 libpng12-dev libpoppler13 libpthread-stubs0 libpthread-stubs0-dev libpython2.6 libsm-dev libsm6 libsqlite3-0 libssl-dev libssl1.0.0 libunistring0 libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxaw7 libxcb1 libxcb1-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxi6 libxml2 libxmu6 libxpm4 libxt-dev libxt6 libxxf86vm1 luatex man-db mesa-common-dev mime-support po-debconf python python-dev python-minimal python-numpy python-support python2.6 python2.6-dev python2.6-minimal sbuild-build-depends-pymol-dummy tcl8.4 tcl8.4-dev tex-common texlive-base texlive-binaries texlive-common texlive-doc-base texlive-latex-base tk8.4 tk8.4-dev ttf-dejavu-core ucf x11-common x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-xext-dev xorg-sgml-doctools xtrans-dev zlib1g-dev 0 upgraded, 109 newly installed, 0 to remove and 0 not upgraded. Need to get 79.0 MB/79.0 MB of archives. After this operation, 225 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libssl1.0.0 libpcre3 libdrm2 libexpat1 libfreetype6 ucf ttf-dejavu-core fontconfig-config libfontconfig1 libgfortran3 libglapi-mesa libxau6 libxdmcp6 libxcb1 libx11-data libx11-6 libxfixes3 libxdamage1 libxext6 libxxf86vm1 libgl1-mesa-glx libglu1-mesa libxi6 x11-common libice6 libsm6 libxt6 libxmu6 libglew1.6 libpng12-0 libdb4.8 bsdmainutils groff-base man-db libmagic1 file gettext-base libsqlite3-0 libxml2 mime-support python2.6-minimal python2.6 python-minimal python python-support html2text libglib2.0-0 libcroco3 libunistring0 gettext intltool-debian po-debconf debhelper dpatch ed freeglut3 xorg-sgml-doctools x11proto-core-dev libxau-dev libxdmcp-dev x11proto-input-dev x11proto-kb-dev xtrans-dev libpthread-stubs0 libpthread-stubs0-dev libxcb1-dev libx11-dev mesa-common-dev x11proto-xext-dev libxext-dev libgl1-mesa-dev libglu1-mesa-dev libice-dev libsm-dev libxt-dev freeglut3-dev libblas3gf zlib1g-dev libfreetype6-dev libglew1.6-dev libjpeg62 libkpathsea5 liblapack3gf liblcms1 libopenjpeg2 libpaper1 libpaper-utils libpng12-dev libpoppler13 libpython2.6 libssl-dev libxpm4 libxaw7 luatex python2.6-dev python-dev python-numpy tcl8.4 tcl8.4-dev tex-common texlive-common texlive-doc-base texlive-binaries texlive-base texlive-latex-base tk8.4 tk8.4-dev sbuild-build-depends-pymol-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-3 [37.9 kB] Get:2 http://localhost/debian/ sid/main libssl1.0.0 amd64 1.0.0e-2 [1143 kB] Get:3 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:4 http://localhost/debian/ sid/main libdrm2 amd64 2.4.26-1 [428 kB] Get:5 http://localhost/debian/ sid/main libexpat1 amd64 2.0.1-7 [137 kB] Get:6 http://localhost/debian/ sid/main libfreetype6 amd64 2.4.6-2 [435 kB] Get:7 http://localhost/debian/ sid/main ucf all 3.0025+nmu2 [70.6 kB] Get:8 http://localhost/debian/ sid/main ttf-dejavu-core all 2.33-2 [1552 kB] Get:9 http://localhost/debian/ sid/main fontconfig-config all 2.8.0-3 [221 kB] Get:10 http://localhost/debian/ sid/main libfontconfig1 amd64 2.8.0-3 [282 kB] Get:11 http://localhost/debian/ sid/main libgfortran3 amd64 4.6.1-10 [358 kB] Get:12 http://localhost/debian/ sid/main libglapi-mesa amd64 7.11-5 [55.1 kB] Get:13 http://localhost/debian/ sid/main libxau6 amd64 1:1.0.6-3 [17.0 kB] Get:14 http://localhost/debian/ sid/main libxdmcp6 amd64 1:1.1.0-3 [22.9 kB] Get:15 http://localhost/debian/ sid/main libxcb1 amd64 1.7-3 [45.4 kB] Get:16 http://localhost/debian/ sid/main libx11-data all 2:1.4.4-1 [183 kB] Get:17 http://localhost/debian/ sid/main libx11-6 amd64 2:1.4.4-1 [889 kB] Get:18 http://localhost/debian/ sid/main libxfixes3 amd64 1:5.0-4 [21.5 kB] Get:19 http://localhost/debian/ sid/main libxdamage1 amd64 1:1.1.3-2 [14.3 kB] Get:20 http://localhost/debian/ sid/main libxext6 amd64 2:1.3.0-3 [52.3 kB] Get:21 http://localhost/debian/ sid/main libxxf86vm1 amd64 1:1.1.1-2 [18.2 kB] Get:22 http://localhost/debian/ sid/main libgl1-mesa-glx amd64 7.11-5 [155 kB] Get:23 http://localhost/debian/ sid/main libglu1-mesa amd64 7.11-5 [220 kB] Get:24 http://localhost/debian/ sid/main libxi6 amd64 2:1.4.3-3 [66.2 kB] Get:25 http://localhost/debian/ sid/main x11-common all 1:7.6+8 [276 kB] Get:26 http://localhost/debian/ sid/main libice6 amd64 2:1.0.7-2 [56.5 kB] Get:27 http://localhost/debian/ sid/main libsm6 amd64 2:1.2.0-2 [29.8 kB] Get:28 http://localhost/debian/ sid/main libxt6 amd64 1:1.1.1-2 [207 kB] Get:29 http://localhost/debian/ sid/main libxmu6 amd64 2:1.1.0-2 [63.5 kB] Get:30 http://localhost/debian/ sid/main libglew1.6 amd64 1.6.0-4 [124 kB] Get:31 http://localhost/debian/ sid/main libpng12-0 amd64 1.2.46-3 [188 kB] Get:32 http://localhost/debian/ sid/main libdb4.8 amd64 4.8.30-9 [694 kB] Get:33 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:34 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:35 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-2 [1023 kB] Get:36 http://localhost/debian/ sid/main libmagic1 amd64 5.08-1 [246 kB] Get:37 http://localhost/debian/ sid/main file amd64 5.08-1 [51.7 kB] Get:38 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-4 [154 kB] Get:39 http://localhost/debian/ sid/main libsqlite3-0 amd64 3.7.7-2 [420 kB] Get:40 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-4 [892 kB] Get:41 http://localhost/debian/ sid/main mime-support all 3.51-1 [35.0 kB] Get:42 http://localhost/debian/ sid/main python2.6-minimal amd64 2.6.7-4 [1524 kB] Get:43 http://localhost/debian/ sid/main python2.6 amd64 2.6.7-4 [2483 kB] Get:44 http://localhost/debian/ sid/main python-minimal all 2.6.7-3 [39.2 kB] Get:45 http://localhost/debian/ sid/main python all 2.6.7-3 [177 kB] Get:46 http://localhost/debian/ sid/main python-support all 1.0.14 [33.5 kB] Get:47 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:48 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.28.6-1 [1648 kB] Get:49 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-1 [125 kB] Get:50 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-4 [437 kB] Get:51 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-4 [2079 kB] Get:52 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:53 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu1 [223 kB] Get:54 http://localhost/debian/ sid/main debhelper all 8.9.6 [562 kB] Get:55 http://localhost/debian/ sid/main dpatch all 2.0.32 [94.8 kB] Get:56 http://localhost/debian/ sid/main ed amd64 1.5-3 [63.1 kB] Get:57 http://localhost/debian/ sid/main freeglut3 amd64 2.6.0-1 [140 kB] Get:58 http://localhost/debian/ sid/main xorg-sgml-doctools all 1:1.8-2 [20.0 kB] Get:59 http://localhost/debian/ sid/main x11proto-core-dev all 7.0.22-1 [323 kB] Get:60 http://localhost/debian/ sid/main libxau-dev amd64 1:1.0.6-3 [20.5 kB] Get:61 http://localhost/debian/ sid/main libxdmcp-dev amd64 1:1.1.0-3 [56.5 kB] Get:62 http://localhost/debian/ sid/main x11proto-input-dev all 2.0.2-2 [82.3 kB] Get:63 http://localhost/debian/ sid/main x11proto-kb-dev all 1.0.5-2 [27.5 kB] Get:64 http://localhost/debian/ sid/main xtrans-dev all 1.2.6-2 [101 kB] Get:65 http://localhost/debian/ sid/main libpthread-stubs0 amd64 0.3-2.1 [3232 B] Get:66 http://localhost/debian/ sid/main libpthread-stubs0-dev amd64 0.3-2.1 [3554 B] Get:67 http://localhost/debian/ sid/main libxcb1-dev amd64 1.7-3 [83.1 kB] Get:68 http://localhost/debian/ sid/main libx11-dev amd64 2:1.4.4-1 [3383 kB] Get:69 http://localhost/debian/ sid/main mesa-common-dev amd64 7.11-5 [342 kB] Get:70 http://localhost/debian/ sid/main x11proto-xext-dev all 7.2.0-3 [255 kB] Get:71 http://localhost/debian/ sid/main libxext-dev amd64 2:1.3.0-3 [167 kB] Get:72 http://localhost/debian/ sid/main libgl1-mesa-dev amd64 7.11-5 [31.1 kB] Get:73 http://localhost/debian/ sid/main libglu1-mesa-dev amd64 7.11-5 [295 kB] Get:74 http://localhost/debian/ sid/main libice-dev amd64 2:1.0.7-2 [143 kB] Get:75 http://localhost/debian/ sid/main libsm-dev amd64 2:1.2.0-2 [101 kB] Get:76 http://localhost/debian/ sid/main libxt-dev amd64 1:1.1.1-2 [512 kB] Get:77 http://localhost/debian/ sid/main freeglut3-dev amd64 2.6.0-1 [215 kB] Get:78 http://localhost/debian/ sid/main libblas3gf amd64 1.2.20110419-2 [292 kB] Get:79 http://localhost/debian/ sid/main zlib1g-dev amd64 1:1.2.3.4.dfsg-3 [192 kB] Get:80 http://localhost/debian/ sid/main libfreetype6-dev amd64 2.4.6-2 [797 kB] Get:81 http://localhost/debian/ sid/main libglew1.6-dev amd64 1.6.0-4 [247 kB] Get:82 http://localhost/debian/ sid/main libjpeg62 amd64 6b1-2 [94.1 kB] Get:83 http://localhost/debian/ sid/main libkpathsea5 amd64 2009-11 [136 kB] Get:84 http://localhost/debian/ sid/main liblapack3gf amd64 3.3.1-1 [4437 kB] Get:85 http://localhost/debian/ sid/main liblcms1 amd64 1.19.dfsg-1 [111 kB] Get:86 http://localhost/debian/ sid/main libopenjpeg2 amd64 1.3+dfsg-4 [79.5 kB] Get:87 http://localhost/debian/ sid/main libpaper1 amd64 1.1.24+nmu1 [21.8 kB] Get:88 http://localhost/debian/ sid/main libpaper-utils amd64 1.1.24+nmu1 [18.1 kB] Get:89 http://localhost/debian/ sid/main libpng12-dev amd64 1.2.46-3 [265 kB] Get:90 http://localhost/debian/ sid/main libpoppler13 amd64 0.16.7-2 [1035 kB] Get:91 http://localhost/debian/ sid/main libpython2.6 amd64 2.6.7-4 [1087 kB] Get:92 http://localhost/debian/ sid/main libssl-dev amd64 1.0.0e-2 [1631 kB] Get:93 http://localhost/debian/ sid/main libxpm4 amd64 1:3.5.9-1 [48.4 kB] Get:94 http://localhost/debian/ sid/main libxaw7 amd64 2:1.0.9-2 [220 kB] Get:95 http://localhost/debian/ sid/main luatex amd64 0.70.1-1+b1 [2469 kB] Get:96 http://localhost/debian/ sid/main python2.6-dev amd64 2.6.7-4 [4832 kB] Get:97 http://localhost/debian/ sid/main python-dev all 2.6.7-3 [914 B] Get:98 http://localhost/debian/ sid/main python-numpy amd64 1:1.5.1-2+b1 [2171 kB] Get:99 http://localhost/debian/ sid/main tcl8.4 amd64 8.4.19-4 [1206 kB] Get:100 http://localhost/debian/ sid/main tcl8.4-dev amd64 8.4.19-4 [829 kB] Get:101 http://localhost/debian/ sid/main tex-common all 2.10 [725 kB] Get:102 http://localhost/debian/ sid/main texlive-common all 2009-13 [101 kB] Get:103 http://localhost/debian/ sid/main texlive-doc-base all 2009-2 [1345 kB] Get:104 http://localhost/debian/ sid/main texlive-binaries amd64 2009-11 [8069 kB] Get:105 http://localhost/debian/ sid/main texlive-base all 2009-13 [14.7 MB] Get:106 http://localhost/debian/ sid/main texlive-latex-base all 2009-13 [1423 kB] Get:107 http://localhost/debian/ sid/main tk8.4 amd64 8.4.19-4 [1053 kB] Get:108 http://localhost/debian/ sid/main tk8.4-dev amd64 8.4.19-4 [880 kB] Extracting templates from packages: 27% Extracting templates from packages: 55% Extracting templates from packages: 82% Extracting templates from packages: 100% Preconfiguring packages ... Fetched 79.0 MB in 1s (63.2 MB/s) Selecting previously deselected package libpipeline1. (Reading database ... 10801 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ... Selecting previously deselected package libssl1.0.0. Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-2_amd64.deb) ... Selecting previously deselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously deselected package libdrm2. Unpacking libdrm2 (from .../libdrm2_2.4.26-1_amd64.deb) ... Selecting previously deselected package libexpat1. Unpacking libexpat1 (from .../libexpat1_2.0.1-7_amd64.deb) ... Selecting previously deselected package libfreetype6. Unpacking libfreetype6 (from .../libfreetype6_2.4.6-2_amd64.deb) ... Selecting previously deselected package ucf. Unpacking ucf (from .../ucf_3.0025+nmu2_all.deb) ... Moving old data out of the way Selecting previously deselected package ttf-dejavu-core. 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Setting up libdb4.8 (4.8.30-9) ... 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 groff-base (1.21-6) ... Setting up man-db (2.6.0.2-2) ... Building database of manual pages ... Setting up libmagic1 (5.08-1) ... Setting up file (5.08-1) ... Setting up gettext-base (0.18.1.1-4) ... Setting up libsqlite3-0 (3.7.7-2) ... Setting up libxml2 (2.7.8.dfsg-4) ... Setting up mime-support (3.51-1) ... Setting up python2.6-minimal (2.6.7-4) ... Setting up python2.6 (2.6.7-4) ... Setting up python-minimal (2.6.7-3) ... Setting up python (2.6.7-3) ... Setting up python-support (1.0.14) ... Setting up html2text (1.3.2a-15) ... Setting up libglib2.0-0 (2.28.6-1) ... No schema files found: doing nothing. Setting up libcroco3 (0.6.2-1) ... Setting up libunistring0 (0.9.3-4) ... Setting up gettext (0.18.1.1-4) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu1) ... Setting up debhelper (8.9.6) ... Setting up dpatch (2.0.32) ... Setting up ed (1.5-3) ... Setting up freeglut3 (2.6.0-1) ... Setting up xorg-sgml-doctools (1:1.8-2) ... Setting up x11proto-core-dev (7.0.22-1) ... Setting up libxau-dev (1:1.0.6-3) ... Setting up libxdmcp-dev (1:1.1.0-3) ... Setting up x11proto-input-dev (2.0.2-2) ... Setting up x11proto-kb-dev (1.0.5-2) ... Setting up xtrans-dev (1.2.6-2) ... Setting up libpthread-stubs0 (0.3-2.1) ... Setting up libpthread-stubs0-dev (0.3-2.1) ... Setting up libxcb1-dev (1.7-3) ... Setting up libx11-dev (2:1.4.4-1) ... Setting up mesa-common-dev (7.11-5) ... Setting up x11proto-xext-dev (7.2.0-3) ... Setting up libxext-dev (2:1.3.0-3) ... Setting up libgl1-mesa-dev (7.11-5) ... Setting up libglu1-mesa-dev (7.11-5) ... Setting up libice-dev (2:1.0.7-2) ... Setting up libsm-dev (2:1.2.0-2) ... Setting up libxt-dev (1:1.1.1-2) ... Setting up freeglut3-dev (2.6.0-1) ... 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 zlib1g-dev (1:1.2.3.4.dfsg-3) ... Setting up libfreetype6-dev (2.4.6-2) ... Setting up libglew1.6-dev (1.6.0-4) ... Setting up libjpeg62 (6b1-2) ... Setting up libkpathsea5 (2009-11) ... Setting up liblapack3gf (3.3.1-1) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3gf to provide /usr/lib/liblapack.so.3gf (liblapack.so.3gf) in auto mode. Setting up liblcms1 (1.19.dfsg-1) ... Setting up libopenjpeg2 (1.3+dfsg-4) ... Setting up libpaper1 (1.1.24+nmu1) ... Creating config file /etc/papersize with new version Setting up libpaper-utils (1.1.24+nmu1) ... Setting up libpng12-dev (1.2.46-3) ... Setting up libpoppler13 (0.16.7-2) ... Setting up libpython2.6 (2.6.7-4) ... Setting up libssl-dev (1.0.0e-2) ... Setting up libxpm4 (1:3.5.9-1) ... Setting up libxaw7 (2:1.0.9-2) ... Setting up luatex (0.70.1-1+b1) ... texlive-base is not ready, cannot create formats Setting up python2.6-dev (2.6.7-4) ... Setting up python-dev (2.6.7-3) ... Setting up python-numpy (1:1.5.1-2+b1) ... Setting up tcl8.4 (8.4.19-4) ... update-alternatives: using /usr/bin/tclsh8.4 to provide /usr/bin/tclsh (tclsh) in auto mode. Setting up tcl8.4-dev (8.4.19-4) ... Setting up tex-common (2.10) ... Creating config file /etc/texmf/texmf.d/05TeXMF.cnf with new version Creating config file /etc/texmf/texmf.d/15Plain.cnf with new version Creating config file /etc/texmf/texmf.d/45TeXinputs.cnf with new version Creating config file /etc/texmf/texmf.d/55Fonts.cnf with new version Creating config file /etc/texmf/texmf.d/65BibTeX.cnf with new version Creating config file /etc/texmf/texmf.d/75DviPS.cnf with new version Creating config file /etc/texmf/texmf.d/80DVIPDFMx.cnf with new version Creating config file /etc/texmf/texmf.d/85Misc.cnf with new version Creating config file /etc/texmf/texmf.d/90TeXDoc.cnf with new version Creating config file /etc/texmf/texmf.d/95NonPath.cnf with new version Creating config file /etc/texmf/updmap.d/00updmap.cfg with new version Creating config file /etc/texmf/texmf.cnf with new version Running mktexlsr. This may take some time... done. texlive-base is not ready, delaying updmap-sys call texlive-base is not ready, skipping fmtutil-sys --all call Setting up texlive-common (2009-13) ... Setting up texlive-doc-base (2009-2) ... Setting up texlive-binaries (2009-11) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode. update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode. Building format(s) --refresh. This may take some time... done. Setting up tk8.4 (8.4.19-4) ... update-alternatives: using /usr/bin/wish8.4 to provide /usr/bin/wish (wish) in auto mode. Setting up tk8.4-dev (8.4.19-4) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Setting up texlive-base (2009-13) ... Creating config file /etc/texmf/dvips/config/config.ps with new version Creating config file /etc/texmf/tex/generic/config/pdftexconfig.tex with new version Creating config file /etc/texmf/dvipdfmx/dvipdfmx.cfg with new version Creating config file /etc/texmf/xdvi/XDvi with new version Running mktexlsr. This may take some time... done. Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-base.cnf. This may take some time... done. Processing triggers for tex-common ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building e-tex based formats --byhyphen /var/lib/texmf/tex/generic/config/language.def. This may take some time... done. Setting up texlive-latex-base (2009-13) ... Running mktexlsr. This may take some time... done. Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-latex-base.cnf. This may take some time... done. Processing triggers for tex-common ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up sbuild-build-depends-pymol-dummy (0.invalid.0) ... Processing triggers for python-support ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-10 gcc-4.6_4.6.1-10 libc6-dev_2.13-20 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 linux-libc-dev_3.0.0-3 Package versions: apt_0.8.15.6 apt-utils_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 clang_2.9-11 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-10 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffutils_1:3.0-1 dpatch_2.0.32 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 ed_1.5-3 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig-config_2.8.0-3 freeglut3_2.6.0-1 freeglut3-dev_2.6.0-1 g++_4:4.6.1-2 g++-4.6_4.6.1-10 gcc_4:4.6.1-2 gcc-4.6_4.6.1-10 gcc-4.6-base_4.6.1-10 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblas3gf_1.2.20110419-2 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc6_2.13-20 libc6-dev_2.13-20 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb4.8_4.8.30-9 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libdrm2_2.4.26-1 libexpat1_2.0.1-7 libffi5_3.0.10~rc10-3 libfontconfig1_2.8.0-3 libfreetype6_2.4.6-2 libfreetype6-dev_2.4.6-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-10 libgdbm3_1.8.3-10 libgfortran3_4.6.1-10 libgl1-mesa-dev_7.11-5 libgl1-mesa-glx_7.11-5 libglapi-mesa_7.11-5 libglew1.6_1.6.0-4 libglew1.6-dev_1.6.0-4 libglib2.0-0_2.28.6-1 libglu1-mesa_7.11-5 libglu1-mesa-dev_7.11-5 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-10 libice-dev_2:1.0.7-2 libice6_2:1.0.7-2 libjpeg62_6b1-2 libkpathsea5_2009-11 liblapack3gf_3.3.1-1 liblcms1_1.19.dfsg-1 libllvm2.9_2.9+dfsg-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libopenjpeg2_1.3+dfsg-4 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpaper-utils_1.1.24+nmu1 libpaper1_1.1.24+nmu1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpng12-dev_1.2.46-3 libpoppler13_0.16.7-2 libpthread-stubs0_0.3-2.1 libpthread-stubs0-dev_0.3-2.1 libpython2.6_2.6.7-4 libquadmath0_4.6.1-10 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libsm-dev_2:1.2.0-2 libsm6_2:1.2.0-2 libsqlite3-0_3.7.7-2 libss2_1.42~WIP-2011-07-02-1 libssl-dev_1.0.0e-2 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-10 libstdc++6-4.6-dev_4.6.1-10 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libx11-6_2:1.4.4-1 libx11-data_2:1.4.4-1 libx11-dev_2:1.4.4-1 libxau-dev_1:1.0.6-3 libxau6_1:1.0.6-3 libxaw7_2:1.0.9-2 libxcb1_1.7-3 libxcb1-dev_1.7-3 libxdamage1_1:1.1.3-2 libxdmcp-dev_1:1.1.0-3 libxdmcp6_1:1.1.0-3 libxext-dev_2:1.3.0-3 libxext6_2:1.3.0-3 libxfixes3_1:5.0-4 libxi6_2:1.4.3-3 libxml2_2.7.8.dfsg-4 libxmu6_2:1.1.0-2 libxpm4_1:3.5.9-1 libxt-dev_1:1.1.1-2 libxt6_1:1.1.1-2 libxxf86vm1_1:1.1.1-2 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 luatex_0.70.1-1+b1 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mesa-common-dev_7.11-5 mime-support_3.51-1 mount_2.19.1-5 multiarch-support_2.13-20 ncurses-base_5.9-1 ncurses-bin_5.9-1 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 python_2.6.7-3 python-dev_2.6.7-3 python-minimal_2.6.7-3 python-numpy_1:1.5.1-2+b1 python-support_1.0.14 python2.6_2.6.7-4 python2.6-dev_2.6.7-4 python2.6-minimal_2.6.7-4 readline-common_6.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pymol-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tcl8.4_8.4.19-4 tcl8.4-dev_8.4.19-4 tex-common_2.10 texlive-base_2009-13 texlive-binaries_2009-11 texlive-common_2009-13 texlive-doc-base_2009-2 texlive-latex-base_2009-13 tk8.4_8.4.19-4 tk8.4-dev_8.4.19-4 ttf-dejavu-core_2.33-2 tzdata_2011i-2 ucf_3.0025+nmu2 util-linux_2.19.1-5 x11-common_1:7.6+8 x11proto-core-dev_7.0.22-1 x11proto-input-dev_2.0.2-2 x11proto-kb-dev_1.0.5-2 x11proto-xext-dev_7.2.0-3 xorg-sgml-doctools_1:1.8-2 xtrans-dev_1.2.6-2 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Sat Aug 27 19:40:12 2011 CEST using DSA key ID 9ED101BF gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./pymol_1.4.1-1.dsc dpkg-source: info: extracting pymol in pymol-1.4.1 dpkg-source: info: unpacking pymol_1.4.1.orig.tar.gz dpkg-source: info: applying pymol_1.4.1-1.diff.gz Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── 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): dpkg-buildpackage: source package pymol dpkg-buildpackage: source version 1.4.1-1 dpkg-source --before-build pymol-1.4.1 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dpatch deapply-all 24_autodock_plugin not applied to ./ . 23_bts576210_FTBFS_ia64 not applied to ./ . 22_fix_pymol_import not applied to ./ . 21_fix_png_batch_mode not applied to ./ . 20_output_license_terms not applied to ./ . 19_blosum_matrix_path not applied to ./ . 17_cmyk_png_data_path not applied to ./ . 13_activate_vmd_plugin not applied to ./ . 11_fix__cmd_import not applied to ./ . 09_chempy_data_path not applied to ./ . 05_examples_data_path not applied to ./ . 03_povray not applied to ./ . 02_test-suite not applied to ./ . rm -rf patch-stamp patch-stampT debian/patched dh_testdir dh_testroot [ ! -f Makefile ] || /usr/bin/make distclean python setup.py clean running clean After running: python setup.py install Please run, to complete the installation: python setup2.py install To uninstall PyMOL, run: python setup2.py uninstall rm -rf build test/tmp test/cmp dh_clean build-stamp install-stamp debian/pymol.launch \ debian/pymol-ref-card.* Rules.make test/pymol-test dpkg-source -b pymol-1.4.1 dpkg-source: warning: no source format specified in debian/source/format, see dpkg-source(1) dpkg-source: info: using source format `1.0' dpkg-source: info: building pymol using existing pymol_1.4.1.orig.tar.gz dpkg-source: info: building pymol in pymol_1.4.1-1.diff.gz dpkg-source: warning: executable mode 0755 of 'debian/patches/17_cmyk_png_data_path.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/22_fix_pymol_import.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/23_bts576210_FTBFS_ia64.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/13_activate_vmd_plugin.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/19_blosum_matrix_path.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/21_fix_png_batch_mode.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/03_povray.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/05_examples_data_path.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/24_autodock_plugin.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/02_test-suite.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/09_chempy_data_path.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/20_output_license_terms.dpatch' will not be represented in diff dpkg-source: warning: executable mode 0755 of 'debian/patches/11_fix__cmd_import.dpatch' will not be represented in diff dpkg-source: info: building pymol in pymol_1.4.1-1.dsc debian/rules build test -d debian/patched || install -d debian/patched dpatch apply-all applying patch 02_test-suite to ./ ... ok. applying patch 03_povray to ./ ... ok. applying patch 05_examples_data_path to ./ ... ok. applying patch 09_chempy_data_path to ./ ... ok. applying patch 11_fix__cmd_import to ./ ... ok. applying patch 13_activate_vmd_plugin to ./ ... ok. applying patch 17_cmyk_png_data_path to ./ ... ok. applying patch 19_blosum_matrix_path to ./ ... ok. applying patch 20_output_license_terms to ./ ... ok. applying patch 21_fix_png_batch_mode to ./ ... ok. applying patch 22_fix_pymol_import to ./ ... ok. applying patch 23_bts576210_FTBFS_ia64 to ./ ... ok. applying patch 24_autodock_plugin to ./ ... ok. dpatch cat-all >>patch-stampT mv -f patch-stampT patch-stamp dh_testdir python setup.py build running build running build_py creating build creating build/lib.linux-x86_64-2.6 creating build/lib.linux-x86_64-2.6/chempy copying modules/chempy/mol2.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/hetatm.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/pkl.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/mae.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/cpv.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/protein.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/solvate.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/mass.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/bonds.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/__init__.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/neighbor.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/cif.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/mmd.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/dictdb.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/cc1.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/water_amber.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/protein_amber.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/pdb.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/io.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/water_residues.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/cex.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/place.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/bond_amber.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/map.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/bond_mmff.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/brick.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/lst.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/protein_mmff.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/protein_residues.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/sdf.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/gms.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/protein_amber99.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/xyz.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/models.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/charge.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/mol.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/arc.py -> build/lib.linux-x86_64-2.6/chempy copying modules/chempy/gamess1.py -> build/lib.linux-x86_64-2.6/chempy creating build/lib.linux-x86_64-2.6/chempy/bmin copying modules/chempy/bmin/state.py -> build/lib.linux-x86_64-2.6/chempy/bmin copying modules/chempy/bmin/__init__.py -> build/lib.linux-x86_64-2.6/chempy/bmin copying modules/chempy/bmin/realtime.py -> build/lib.linux-x86_64-2.6/chempy/bmin copying modules/chempy/bmin/util.py -> build/lib.linux-x86_64-2.6/chempy/bmin copying modules/chempy/bmin/commands.py -> build/lib.linux-x86_64-2.6/chempy/bmin creating build/lib.linux-x86_64-2.6/chempy/champ copying modules/chempy/champ/formal_charges.py -> build/lib.linux-x86_64-2.6/chempy/champ copying modules/chempy/champ/__init__.py -> build/lib.linux-x86_64-2.6/chempy/champ copying modules/chempy/champ/amber99.py -> build/lib.linux-x86_64-2.6/chempy/champ copying modules/chempy/champ/assign.py -> build/lib.linux-x86_64-2.6/chempy/champ creating build/lib.linux-x86_64-2.6/chempy/fast copying modules/chempy/fast/__init__.py -> build/lib.linux-x86_64-2.6/chempy/fast creating build/lib.linux-x86_64-2.6/chempy/fragments copying modules/chempy/fragments/__init__.py -> build/lib.linux-x86_64-2.6/chempy/fragments creating build/lib.linux-x86_64-2.6/chempy/tinker copying modules/chempy/tinker/__init__.py -> build/lib.linux-x86_64-2.6/chempy/tinker copying modules/chempy/tinker/state.py -> build/lib.linux-x86_64-2.6/chempy/tinker copying modules/chempy/tinker/realtime.py -> build/lib.linux-x86_64-2.6/chempy/tinker copying modules/chempy/tinker/keyword.py -> build/lib.linux-x86_64-2.6/chempy/tinker copying modules/chempy/tinker/amber.py -> build/lib.linux-x86_64-2.6/chempy/tinker creating build/lib.linux-x86_64-2.6/pmg_tk copying modules/pmg_tk/Setting.py -> build/lib.linux-x86_64-2.6/pmg_tk copying modules/pmg_tk/SetEditor.py -> build/lib.linux-x86_64-2.6/pmg_tk copying modules/pmg_tk/__init__.py -> build/lib.linux-x86_64-2.6/pmg_tk copying modules/pmg_tk/PMGApp.py -> build/lib.linux-x86_64-2.6/pmg_tk copying modules/pmg_tk/Demo.py -> build/lib.linux-x86_64-2.6/pmg_tk copying modules/pmg_tk/ColorEditor.py -> build/lib.linux-x86_64-2.6/pmg_tk creating build/lib.linux-x86_64-2.6/pmg_tk/startup copying modules/pmg_tk/startup/autodock.py -> build/lib.linux-x86_64-2.6/pmg_tk/startup copying modules/pmg_tk/startup/remote_pdb_load.py -> build/lib.linux-x86_64-2.6/pmg_tk/startup copying modules/pmg_tk/startup/__init__.py -> build/lib.linux-x86_64-2.6/pmg_tk/startup copying modules/pmg_tk/startup/apbs_tools.py -> build/lib.linux-x86_64-2.6/pmg_tk/startup creating build/lib.linux-x86_64-2.6/pmg_tk/skins copying modules/pmg_tk/skins/__init__.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins creating build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/__init__.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/volume.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ColorRampModel.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ModalWindow.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ColorMap.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/builder.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/SimpleColorChooser.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/hist.py -> build/lib.linux-x86_64-2.6/pmg_tk/skins/normal creating build/lib.linux-x86_64-2.6/pmg_wx copying modules/pmg_wx/__init__.py -> build/lib.linux-x86_64-2.6/pmg_wx creating build/lib.linux-x86_64-2.6/pymol copying modules/pymol/__init__.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/exporting.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/fitting.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/importing.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/povray.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/shortcut.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/viewing.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/computing.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/menu.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/feedingback.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/colorramping.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/vfont.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/moving.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/headering.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/setting.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/invocation.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/externing.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/completing.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/locking.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/editing.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/movie.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/checking.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/experimenting.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/parsing.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/m4x.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/selector.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/xray.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/util.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/keywords.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/creating.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/commanding.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/cmd.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/cgo.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/rpc.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/selecting.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/callback.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/parser.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/controlling.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/keyboard.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/api.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/gui.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/constants.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/monitoring.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/internal.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/helping.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/xwin.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/wizarding.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/editor.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/preset.py -> build/lib.linux-x86_64-2.6/pymol copying modules/pymol/querying.py -> build/lib.linux-x86_64-2.6/pymol creating build/lib.linux-x86_64-2.6/pymol/contrib copying modules/pymol/contrib/__init__.py -> build/lib.linux-x86_64-2.6/pymol/contrib creating build/lib.linux-x86_64-2.6/pymol/opengl copying modules/pymol/opengl/__init__.py -> build/lib.linux-x86_64-2.6/pymol/opengl creating build/lib.linux-x86_64-2.6/pymol/opengl/gl copying modules/pymol/opengl/gl/__init__.py -> build/lib.linux-x86_64-2.6/pymol/opengl/gl copying modules/pymol/opengl/gl/glconst.py -> build/lib.linux-x86_64-2.6/pymol/opengl/gl creating build/lib.linux-x86_64-2.6/pymol/opengl/glu copying modules/pymol/opengl/glu/__init__.py -> build/lib.linux-x86_64-2.6/pymol/opengl/glu copying modules/pymol/opengl/glu/gluconst.py -> build/lib.linux-x86_64-2.6/pymol/opengl/glu creating build/lib.linux-x86_64-2.6/pymol/opengl/glut copying modules/pymol/opengl/glut/__init__.py -> build/lib.linux-x86_64-2.6/pymol/opengl/glut copying modules/pymol/opengl/glut/glutconst.py -> build/lib.linux-x86_64-2.6/pymol/opengl/glut creating build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/mutagenesis.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/demo.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/toggle.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/message.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/filter.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/density.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/distance.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/appearance.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/measurement.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/cleanup.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/__init__.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/dragging.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/sculpting.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/security.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/pseudoatom.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/annotation.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/fedora.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/pair_fit.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/stereodemo.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/charge.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/renaming.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/benchmark.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/box.py -> build/lib.linux-x86_64-2.6/pymol/wizard copying modules/pymol/wizard/label.py -> build/lib.linux-x86_64-2.6/pymol/wizard creating build/lib.linux-x86_64-2.6/web copying modules/web/__init__.py -> build/lib.linux-x86_64-2.6/web copying modules/web/pymolhttpd.py -> build/lib.linux-x86_64-2.6/web creating build/lib.linux-x86_64-2.6/web/examples copying modules/web/examples/__init__.py -> build/lib.linux-x86_64-2.6/web/examples copying modules/web/examples/justhttpd.py -> build/lib.linux-x86_64-2.6/web/examples package init file 'modules/web/javascript/__init__.py' not found (or not a regular file) package init file 'modules/web/javascript/__init__.py' not found (or not a regular file) running build_ext building 'pymol._cmd' extension creating build/temp.linux-x86_64-2.6 creating build/temp.linux-x86_64-2.6/modules creating build/temp.linux-x86_64-2.6/modules/cealign creating build/temp.linux-x86_64-2.6/modules/cealign/src creating build/temp.linux-x86_64-2.6/ov creating build/temp.linux-x86_64-2.6/ov/src creating build/temp.linux-x86_64-2.6/layer0 creating build/temp.linux-x86_64-2.6/layer1 creating build/temp.linux-x86_64-2.6/layer2 creating build/temp.linux-x86_64-2.6/layer3 creating build/temp.linux-x86_64-2.6/layer4 creating build/temp.linux-x86_64-2.6/layer5 creating build/temp.linux-x86_64-2.6/contrib creating build/temp.linux-x86_64-2.6/contrib/uiuc creating build/temp.linux-x86_64-2.6/contrib/uiuc/plugins creating build/temp.linux-x86_64-2.6/contrib/uiuc/plugins/molfile_plugin creating build/temp.linux-x86_64-2.6/contrib/uiuc/plugins/molfile_plugin/src gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_VMD_PLUGINS -DNO_MMLIBS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c modules/cealign/src/ccealignmodule.cpp -o build/temp.linux-x86_64-2.6/modules/cealign/src/ccealignmodule.o -ffast-math -funroll-loops -O3 In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:41: modules/cealign/src/tnt/tnt_array1d.h:238:28: warning: '&&' within '||' [-Wlogical-op-parentheses] if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) ~~~~~~~~~~~~~~~~~~~~~ ^ modules/cealign/src/tnt/tnt_array1d.h:238:28: note: place parentheses around the '&&' expression to silence this warning if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) ^ ( ) In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:48: modules/cealign/src/tnt/tnt_fortran_array1d.h:224:28: warning: '&&' within '||' [-Wlogical-op-parentheses] if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) ~~~~~~~~~~~~~~~~~~~~~ ^ modules/cealign/src/tnt/tnt_fortran_array1d.h:224:28: note: place parentheses around the '&&' expression to silence this warning if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) ^ ( ) In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:55: modules/cealign/src/tnt/tnt_sparse_matrix_csr.h:97:3: error: no matching constructor for initialization of 'Array1D' rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {} ^ ~~~~ In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:41: modules/cealign/src/tnt/tnt_array1d.h:63:11: note: candidate constructor not viable: no known conversion from 'const int *' to 'const int' for 2nd argument Array1D(int n, const T &a); ^ modules/cealign/src/tnt/tnt_array1d.h:64:11: note: candidate constructor not viable: 2nd argument ('const int *') would lose const qualifier Array1D(int n, T *a); ^ modules/cealign/src/tnt/tnt_array1d.h:61:11: note: candidate constructor not viable: requires 0 arguments, but 2 were provided Array1D(); ^ modules/cealign/src/tnt/tnt_array1d.h:62:11: note: candidate constructor not viable: requires 1 argument, but 2 were provided explicit Array1D(int n); ^ modules/cealign/src/tnt/tnt_array1d.h:65:14: note: candidate constructor not viable: requires 1 argument, but 2 were provided inline Array1D(const Array1D &A); ^ In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:55: modules/cealign/src/tnt/tnt_sparse_matrix_csr.h:97:18: error: no matching constructor for initialization of 'Array1D' rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {} ^ ~~~~~ In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:41: modules/cealign/src/tnt/tnt_array1d.h:63:11: note: candidate constructor not viable: no known conversion from 'const int *' to 'const int' for 2nd argument Array1D(int n, const T &a); ^ modules/cealign/src/tnt/tnt_array1d.h:64:11: note: candidate constructor not viable: 2nd argument ('const int *') would lose const qualifier Array1D(int n, T *a); ^ modules/cealign/src/tnt/tnt_array1d.h:61:11: note: candidate constructor not viable: requires 0 arguments, but 2 were provided Array1D(); ^ modules/cealign/src/tnt/tnt_array1d.h:62:11: note: candidate constructor not viable: requires 1 argument, but 2 were provided explicit Array1D(int n); ^ modules/cealign/src/tnt/tnt_array1d.h:65:14: note: candidate constructor not viable: requires 1 argument, but 2 were provided inline Array1D(const Array1D &A); ^ In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:57: In file included from layer0/os_python.h:30: In file included from /usr/include/python2.6/Python.h:8: /usr/include/python2.6/pyconfig.h:1031:9: warning: '_POSIX_C_SOURCE' macro redefined #define _POSIX_C_SOURCE 200112L ^ In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:40: In file included from modules/cealign/src/tnt/tnt_math_utils.h:5: In file included from /usr/include/c++/4.6/cmath:42: In file included from /usr/include/c++/4.6//x86_64-linux-gnu/bits/c++config.h:392: In file included from /usr/include/c++/4.6//x86_64-linux-gnu/bits/os_defines.h:40: /usr/include/features.h:163:10: note: previous definition is here # define _POSIX_C_SOURCE 200809L ^ In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:57: In file included from layer0/os_python.h:30: In file included from /usr/include/python2.6/Python.h:8: /usr/include/python2.6/pyconfig.h:1040:9: warning: '_XOPEN_SOURCE' macro redefined #define _XOPEN_SOURCE 600 ^ In file included from modules/cealign/src/ccealignmodule.cpp:32: In file included from modules/cealign/src/ccealignmodule.H:36: In file included from modules/cealign/src/tnt/tnt.h:40: In file included from modules/cealign/src/tnt/tnt_math_utils.h:5: In file included from /usr/include/c++/4.6/cmath:42: In file included from /usr/include/c++/4.6//x86_64-linux-gnu/bits/c++config.h:392: In file included from /usr/include/c++/4.6//x86_64-linux-gnu/bits/os_defines.h:40: /usr/include/features.h:165:10: note: previous definition is here # define _XOPEN_SOURCE 700 ^ 4 warnings and 2 errors generated. error: command 'gcc' failed with exit status 1 make: *** [build-stamp] Error 1 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20110911-1313 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64c-e268e09c-c30e-4a11-990b-eb263208303d/build/pymol-Z8VmKP Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 47364 Build-Time: 3 Distribution: lsid64c Fail-Stage: build Install-Time: 18 Job: pymol_1.4.1-1 Package: pymol Package-Time: 32 Source-Version: 1.4.1-1 Space: 47364 Status: attempted Version: 1.4.1-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20110911-1313 Build needed 00:00:32, 47364k disc space DC-Build-Status: Failed 1361.764174s ### Content of /var/log/daemon.log ### Sep 11 10:47:48 talc-101 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:47:59 talc-101 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:48:10 talc-101 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:48:34 talc-101 approx: Concurrent download of debian/dists/sid/main/source/Sources.xz is taking too long Sep 11 10:48:42 talc-101 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:48:45 talc-101 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:48:47 talc-101 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:48:56 talc-101 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:48:59 talc-101 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en is taking too long Sep 11 10:49:07 talc-101 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:49:22 talc-101 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:49:22 talc-101 approx: Concurrent download of debian/dists/sid/main/source/Sources.xz is taking too long Sep 11 10:49:33 talc-101 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:49:43 talc-101 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:49:48 talc-101 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:49:54 talc-101 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:49:59 talc-101 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:50:10 talc-101 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:50:15 talc-101 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en.gz is taking too long Sep 11 10:50:21 talc-101 approx: Concurrent download of debian/dists/sid/main/i18n/Index is taking too long Sep 11 10:51:11 talc-101 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en.bz2 is taking too long Sep 11 10:51:22 talc-101 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long Sep 11 10:51:34 talc-101 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en.xz is taking too long Sep 11 10:51:50 talc-101 approx: Concurrent download of debian/dists/sid/main/i18n/Translation-en is taking too long ### End of content of /var/log/daemon.log ### DC-Time-Estimation: 1361.764174 versus expected 239 (r/m: 4.69775805020921 ; m: 239.0) DC-Build-Network: USED. See /tmp/rulesafter.iGOcvf ! ************************************************************ # Generated by iptables-save v1.4.8 on Sun Sep 11 13:13:04 2011 *filter :INPUT ACCEPT [2883724:14623237068] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] [1016598:12668241087] -A OUTPUT -o lo -j ACCEPT [0:0] -A OUTPUT -d 129.88.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 10.0.0.0/8 -j ACCEPT [0:0] -A OUTPUT -d 192.168.133.0/24 -j ACCEPT [0:0] -A OUTPUT -d 192.168.159.0/24 -j ACCEPT [0:0] -A OUTPUT -d 192.168.160.0/24 -j ACCEPT [0:0] -A OUTPUT -d 10.69.0.0/17 -j ACCEPT [0:0] -A OUTPUT -d 172.28.52.0/22 -j ACCEPT [0:0] -A OUTPUT -d 172.24.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 131.254.202.0/23 -j ACCEPT [0:0] -A OUTPUT -d 138.96.20.0/22 -j ACCEPT [0:0] -A OUTPUT -d 192.168.22.0/24 -j ACCEPT [642368:84459845] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT [4098:395412] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT [12:720] -A OUTPUT -j LD [12:720] -A LD -j LOG [12:720] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT # Completed on Sun Sep 11 13:13:04 2011 ************************************************************ --- /tmp/rulesbefore.DgSolJ 2011-09-11 12:50:22.835417761 +0200 +++ /tmp/rulesafter.iGOcvf 2011-09-11 13:13:04.607416773 +0200 @@ -1,10 +1,10 @@ -# Generated by iptables-save v1.4.8 on Sun Sep 11 12:50:22 2011 +# Generated by iptables-save v1.4.8 on Sun Sep 11 13:13:04 2011 *filter -:INPUT ACCEPT [2644652:13383242273] +:INPUT ACCEPT [2883724:14623237068] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] -[913266:11508916609] -A OUTPUT -o lo -j ACCEPT +[1016598:12668241087] -A OUTPUT -o lo -j ACCEPT [0:0] -A OUTPUT -d 129.88.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 10.0.0.0/8 -j ACCEPT [0:0] -A OUTPUT -d 192.168.133.0/24 -j ACCEPT @@ -16,10 +16,10 @@ [0:0] -A OUTPUT -d 131.254.202.0/23 -j ACCEPT [0:0] -A OUTPUT -d 138.96.20.0/22 -j ACCEPT [0:0] -A OUTPUT -d 192.168.22.0/24 -j ACCEPT -[615085:78591737] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT -[3538:341332] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT +[642368:84459845] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT +[4098:395412] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT [12:720] -A OUTPUT -j LD [12:720] -A LD -j LOG [12:720] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT -# Completed on Sun Sep 11 12:50:22 2011 +# Completed on Sun Sep 11 13:13:04 2011 ************************************************************ [ 11.681794] ioatdma 0000:00:0f.0: irq 58 for MSI/MSI-X [ 11.681796] alloc irq_desc for 59 on node -1 [ 11.681797] alloc kstat_irqs on node -1 [ 11.681800] ioatdma 0000:00:0f.0: irq 59 for MSI/MSI-X [ 11.682250] ACPI: SSDT 00000000bff00f00 0016E (v01 PmRef Cpu3Ist 00003000 INTL 20050228) [ 11.732057] intel_rng: FWH not detected [ 11.755864] processor LNXCPU:03: registered as cooling_device3 [ 11.791442] ACPI: SSDT 00000000bff0106e 0016E (v01 PmRef CPU4Ist 00003000 INTL 20050228) [ 11.841926] processor LNXCPU:04: registered as cooling_device4 [ 11.877554] ACPI: SSDT 00000000bff011dc 0016E (v01 PmRef CPU5Ist 00003000 INTL 20050228) [ 11.927859] processor LNXCPU:05: registered as cooling_device5 [ 11.963398] ACPI: SSDT 00000000bff0134a 0016E (v01 PmRef Cpu6Ist 00003000 INTL 20050228) [ 12.013677] processor LNXCPU:06: registered as cooling_device6 [ 12.049222] ACPI: SSDT 00000000bff014b8 0016E (v01 PmRef Cpu7Ist 00003000 INTL 20050228) [ 12.099550] processor LNXCPU:07: registered as cooling_device7 [ 12.877749] Adding 3911788k swap on /dev/sda1. Priority:-1 extents:1 across:3911788k [ 12.927446] EXT3 FS on sda3, internal journal [ 13.194305] kjournald starting. Commit interval 5 seconds [ 13.227254] EXT3 FS on sda5, internal journal [ 13.253488] EXT3-fs: mounted filesystem with ordered data mode. [ 13.608274] e1000e 0000:0f:00.0: irq 54 for MSI/MSI-X [ 13.664052] e1000e 0000:0f:00.0: irq 54 for MSI/MSI-X [ 13.666179] ADDRCONF(NETDEV_UP): eth0: link is not ready [ 16.807937] e1000e: eth0 NIC Link is Up 1000 Mbps Full Duplex, Flow Control: RX/TX [ 16.857617] ADDRCONF(NETDEV_CHANGE): eth0: link becomes ready [ 27.604006] eth0: no IPv6 routers present [ 403.266966] RPC: Registered udp transport module. [ 403.295244] RPC: Registered tcp transport module. [ 403.323461] RPC: Registered tcp NFSv4.1 backchannel transport module. [ 403.394011] Slow work thread pool: Starting up [ 403.420789] Slow work thread pool: Ready [ 403.444381] FS-Cache: Loaded [ 403.494118] FS-Cache: Netfs 'nfs' registered for caching [ 403.532862] svc: failed to register lockdv1 RPC service (errno 97). [ 432.880943] Adding 296929352k swap on /dev/sda5. Priority:-2 extents:1 across:296929352k [ 456.449527] ip_tables: (C) 2000-2006 Netfilter Core Team [ 2924.264988] IN= OUT=eth0 SRC=172.16.66.101 DST=82.94.164.162 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=30905 DF PROTO=TCP SPT=48027 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2927.353780] IN= OUT=eth0 SRC=172.16.66.101 DST=82.94.164.162 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=30906 DF PROTO=TCP SPT=48027 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2927.626816] IN= OUT=eth0 SRC=172.16.66.101 DST=173.203.107.207 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=37509 DF PROTO=TCP SPT=45305 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2930.717774] IN= OUT=eth0 SRC=172.16.66.101 DST=173.203.107.207 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=37510 DF PROTO=TCP SPT=45305 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2930.899792] IN= OUT=eth0 SRC=172.16.66.101 DST=173.203.107.207 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=8018 DF PROTO=TCP SPT=45306 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2933.989525] IN= OUT=eth0 SRC=172.16.66.101 DST=173.203.107.207 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=8019 DF PROTO=TCP SPT=45306 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2935.696221] IN= OUT=eth0 SRC=172.16.66.101 DST=82.94.164.162 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=41634 DF PROTO=TCP SPT=48030 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2938.789026] IN= OUT=eth0 SRC=172.16.66.101 DST=82.94.164.162 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=41635 DF PROTO=TCP SPT=48030 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2938.882044] IN= OUT=eth0 SRC=172.16.66.101 DST=173.203.107.207 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=46074 DF PROTO=TCP SPT=45308 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2941.973034] IN= OUT=eth0 SRC=172.16.66.101 DST=173.203.107.207 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=46075 DF PROTO=TCP SPT=45308 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2942.066889] IN= OUT=eth0 SRC=172.16.66.101 DST=173.203.107.207 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=10184 DF PROTO=TCP SPT=45309 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2945.156300] IN= OUT=eth0 SRC=172.16.66.101 DST=173.203.107.207 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=10185 DF PROTO=TCP SPT=45309 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 7470.095883] cpp[20062]: segfault at 0 ip 000000000057b5ef sp 00007fff789dd000 error 4 in clang[400000+8e1000] [ 8783.340298] cpp[7625]: segfault at 0 ip 000000000057b5ef sp 00007fff07bfe240 error 4 in clang[400000+8e1000] ************************************************************