lockfile creation failed: exceeded maximum number of lock attempts DC-Build-Header: bowtie 0.12.7-1 / Sun Sep 11 10:47:46 +0200 2011 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 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 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 sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on talc-104.nancy.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ bowtie 0.12.7-1 (amd64) 11 Sep 2011 11:18 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: bowtie Version: 0.12.7-1 Source Version: 0.12.7-1 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 (62.6 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: 'bowtie' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debian-med/trunk/packages/bowtie/trunk Need to get 7517 kB of source archives. Get:1 http://localhost/debian/ sid/main bowtie 0.12.7-1 (dsc) [1389 B] Get:2 http://localhost/debian/ sid/main bowtie 0.12.7-1 (tar) [7511 kB] Get:3 http://localhost/debian/ sid/main bowtie 0.12.7-1 (diff) [4813 B] Fetched 7517 kB in 0s (13.4 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/bowtie-O1zpAH/resolver-V5U0kz/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-470a8d34-fe72-4882-81f1-a847f672dd8f/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 (>= 7.1), help2man 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 (>= 7.1), help2man dpkg-deb: building package `sbuild-build-depends-bowtie-dummy' in `/build/bowtie-O1zpAH/resolver-5L9giJ/apt_archive/sbuild-build-depends-bowtie-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install bowtie 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 file gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libglib2.0-0 liblocale-gettext-perl libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libglib2.0-0 liblocale-gettext-perl libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-bowtie-dummy 0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded. Need to get 9308 kB/9309 kB of archives. After this operation, 27.9 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 liblocale-gettext-perl libpcre3 bsdmainutils groff-base man-db libmagic1 file gettext-base libxml2 html2text libglib2.0-0 libcroco3 libunistring0 gettext intltool-debian po-debconf debhelper help2man sbuild-build-depends-bowtie-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 liblocale-gettext-perl amd64 1.05-7 [22.7 kB] Get:3 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:4 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:5 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:6 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-2 [1023 kB] Get:7 http://localhost/debian/ sid/main libmagic1 amd64 5.08-1 [246 kB] Get:8 http://localhost/debian/ sid/main file amd64 5.08-1 [51.7 kB] Get:9 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-4 [154 kB] Get:10 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-4 [892 kB] Get:11 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:12 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.28.6-1 [1648 kB] Get:13 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-1 [125 kB] Get:14 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-4 [437 kB] Get:15 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-4 [2079 kB] Get:16 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:17 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu1 [223 kB] Get:18 http://localhost/debian/ sid/main debhelper all 8.9.6 [562 kB] Get:19 http://localhost/debian/ sid/main help2man amd64 1.40.4 [89.5 kB] Preconfiguring packages ... Fetched 9308 kB in 0s (44.8 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 liblocale-gettext-perl. Unpacking liblocale-gettext-perl (from .../liblocale-gettext-perl_1.05-7_amd64.deb) ... Selecting previously deselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-2_amd64.deb) ... Selecting previously deselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.08-1_amd64.deb) ... Selecting previously deselected package file. Unpacking file (from .../archives/file_5.08-1_amd64.deb) ... Selecting previously deselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_amd64.deb) ... Selecting previously deselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_amd64.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously deselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_amd64.deb) ... Selecting previously deselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-1_amd64.deb) ... Selecting previously deselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-4_amd64.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-4_amd64.deb) ... Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ... Selecting previously deselected package help2man. Unpacking help2man (from .../help2man_1.40.4_amd64.deb) ... Selecting previously deselected package sbuild-build-depends-bowtie-dummy. Unpacking sbuild-build-depends-bowtie-dummy (from .../sbuild-build-depends-bowtie-dummy.deb) ... Processing triggers for install-info ... Setting up libpipeline1 (1.2.0-3) ... Setting up liblocale-gettext-perl (1.05-7) ... Setting up libpcre3 (8.12-4) ... 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 libxml2 (2.7.8.dfsg-4) ... 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 help2man (1.40.4) ... Setting up sbuild-build-depends-bowtie-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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 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 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 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 help2man_1.40.4 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 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 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libffi5_3.0.10~rc10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-10 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-10 libllvm2.9_2.9+dfsg-3 liblocale-gettext-perl_1.05-7 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 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 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 libss2_1.42~WIP-2011-07-02-1 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 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 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 readline-common_6.2-4 sbuild-build-depends-bowtie-dummy_0.invalid.0 sbuild-build-depends-core-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 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_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 Wed Feb 2 13:49:54 2011 CET using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./bowtie_0.12.7-1.dsc dpkg-source: info: extracting bowtie in bowtie-0.12.7 dpkg-source: info: unpacking bowtie_0.12.7.orig.tar.gz dpkg-source: info: unpacking bowtie_0.12.7-1.debian.tar.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 bowtie dpkg-buildpackage: source version 0.12.7-1 dpkg-source --before-build bowtie-0.12.7 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/build/bowtie-O1zpAH/bowtie-0.12.7' rm -f .bowtie* dh_auto_clean make[2]: Entering directory `/build/bowtie-O1zpAH/bowtie-0.12.7' rm -f bowtie-build bowtie bowtie-inspect bowtie-build-debug bowtie-debug bowtie-inspect-debug \ bowtie_prof \ bowtie-build.exe bowtie.exe bowtie-inspect.exe bowtie-build-debug.exe bowtie-debug.exe bowtie-inspect-debug.exe bowtie_prof.exe \ bowtie-src.zip bowtie-bin.zip rm -f core.* make[2]: Leaving directory `/build/bowtie-O1zpAH/bowtie-0.12.7' make[1]: Leaving directory `/build/bowtie-O1zpAH/bowtie-0.12.7' dh_clean dpkg-source -b bowtie-0.12.7 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building bowtie using existing ./bowtie_0.12.7.orig.tar.gz dpkg-source: info: building bowtie in bowtie_0.12.7-1.debian.tar.gz dpkg-source: info: building bowtie in bowtie_0.12.7-1.dsc debian/rules build dh build dh_testdir dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory `/build/bowtie-O1zpAH/bowtie-0.12.7' /usr/bin/make allall make[2]: Entering directory `/build/bowtie-O1zpAH/bowtie-0.12.7' cat ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp aligner.h aligner_0mm.h aligner_1mm.h aligner_23mm.h aligner_metrics.h aligner_seed_mm.h alphabet.h annot.h assert_helpers.h auto_array.h binary_sa_search.h bitpack.h bitset.h blockwise_sa.h color.h color_dec.h diff_sample.h ebwt.h ebwt_search_backtrack.h ebwt_search_util.h edit.h endian_swap.h filebuf.h formats.h hit.h hit_set.h log.h mm.h multikey_qsort.h pat.h pool.h qual.h random_source.h range.h range_cache.h range_chaser.h range_source.h ref_aligner.h ref_read.h reference.h refmap.h row_chaser.h sam.h search_globals.h sequence_io.h shmem.h spinlock.h str_util.h threading.h timer.h tokenize.h word_io.h zbox.h | md5sum | awk '{print $1}' > .bowtie-build.md5 /usr/bin/g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -g -O2 -g -O2 \"" -Wl,--hash-style=both -g -O2 -g -O2 \ -DEBWT_BUILD_HASH=`cat .bowtie-build.md5` \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \ -I SeqAn-1.1 \ -o bowtie-build ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp bowtie_build_main.cpp \ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated In file included from ebwt_build.cpp:11: ./ebwt.h:1501:1: warning: struct 'SideLocus' was previously declared as a class [-Wmismatched-tags] struct SideLocus { ^~~~~~ class ./ebwt.h:306:7: note: previous use is here class SideLocus; ^ ./ebwt.h:3938:11: error: default arguments cannot be added to an out-of-line definition of a member of a class template uint32_t seed = 0) ^ ~ In file included from ebwt_build.cpp:11: In file included from ./ebwt.h:24: ./alphabet.h:48:3: error: use of undeclared identifier 'reverseInPlace' reverseInPlace(s); ^ In file included from ebwt_build.cpp:11: In file included from ./ebwt.h:31: ./hit.h:97:4: note: in instantiation of function template specialization 'reverseComplementInPlace, seqan::Alloc > >' requested here reverseComplementInPlace(hs.seq, hs.color); ^ 1 warning and 2 errors generated. make[2]: *** [bowtie-build] Error 1 make[2]: Leaving directory `/build/bowtie-O1zpAH/bowtie-0.12.7' make[1]: *** [override_dh_auto_build] Error 2 make[1]: Leaving directory `/build/bowtie-O1zpAH/bowtie-0.12.7' make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20110911-1119 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64c-470a8d34-fe72-4882-81f1-a847f672dd8f/build/bowtie-O1zpAH Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 16232 Build-Time: 3 Distribution: lsid64c Fail-Stage: build Install-Time: 4 Job: bowtie_0.12.7-1 Package: bowtie Package-Time: 18 Source-Version: 0.12.7-1 Space: 16232 Status: attempted Version: 0.12.7-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20110911-1119 Build needed 00:00:18, 16232k disc space DC-Message: Failed, but took only 1881.051078. 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 Requested exclusive mode, but other builds running. sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on talc-104.nancy.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ bowtie 0.12.7-1 (amd64) 11 Sep 2011 11:22 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: bowtie Version: 0.12.7-1 Source Version: 0.12.7-1 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 (63.5 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: 'bowtie' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/svn/debian-med/trunk/packages/bowtie/trunk Need to get 7517 kB of source archives. Get:1 http://localhost/debian/ sid/main bowtie 0.12.7-1 (dsc) [1389 B] Get:2 http://localhost/debian/ sid/main bowtie 0.12.7-1 (tar) [7511 kB] Get:3 http://localhost/debian/ sid/main bowtie 0.12.7-1 (diff) [4813 B] Fetched 7517 kB in 0s (60.7 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/bowtie-aTU5lq/resolver-KAUAg0/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-7e19ce3e-f1a6-4a93-965d-c53f058fbb65/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 (>= 7.1), help2man 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 (>= 7.1), help2man dpkg-deb: building package `sbuild-build-depends-bowtie-dummy' in `/build/bowtie-aTU5lq/resolver-2y2Jai/apt_archive/sbuild-build-depends-bowtie-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install bowtie 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 file gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libglib2.0-0 liblocale-gettext-perl libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base help2man html2text intltool-debian libcroco3 libglib2.0-0 liblocale-gettext-perl libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-bowtie-dummy 0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded. Need to get 9308 kB/9309 kB of archives. After this operation, 27.9 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 liblocale-gettext-perl libpcre3 bsdmainutils groff-base man-db libmagic1 file gettext-base libxml2 html2text libglib2.0-0 libcroco3 libunistring0 gettext intltool-debian po-debconf debhelper help2man sbuild-build-depends-bowtie-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 liblocale-gettext-perl amd64 1.05-7 [22.7 kB] Get:3 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:4 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:5 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:6 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-2 [1023 kB] Get:7 http://localhost/debian/ sid/main libmagic1 amd64 5.08-1 [246 kB] Get:8 http://localhost/debian/ sid/main file amd64 5.08-1 [51.7 kB] Get:9 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-4 [154 kB] Get:10 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-4 [892 kB] Get:11 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:12 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.28.6-1 [1648 kB] Get:13 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-1 [125 kB] Get:14 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-4 [437 kB] Get:15 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-4 [2079 kB] Get:16 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:17 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu1 [223 kB] Get:18 http://localhost/debian/ sid/main debhelper all 8.9.6 [562 kB] Get:19 http://localhost/debian/ sid/main help2man amd64 1.40.4 [89.5 kB] Preconfiguring packages ... Fetched 9308 kB in 0s (61.3 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 liblocale-gettext-perl. Unpacking liblocale-gettext-perl (from .../liblocale-gettext-perl_1.05-7_amd64.deb) ... Selecting previously deselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously deselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ... Selecting previously deselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ... Selecting previously deselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-2_amd64.deb) ... Selecting previously deselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.08-1_amd64.deb) ... Selecting previously deselected package file. Unpacking file (from .../archives/file_5.08-1_amd64.deb) ... Selecting previously deselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_amd64.deb) ... Selecting previously deselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_amd64.deb) ... Selecting previously deselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously deselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_amd64.deb) ... Selecting previously deselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-1_amd64.deb) ... Selecting previously deselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-4_amd64.deb) ... Selecting previously deselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-4_amd64.deb) ... Selecting previously deselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously deselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ... Selecting previously deselected package debhelper. Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ... Selecting previously deselected package help2man. Unpacking help2man (from .../help2man_1.40.4_amd64.deb) ... Selecting previously deselected package sbuild-build-depends-bowtie-dummy. Unpacking sbuild-build-depends-bowtie-dummy (from .../sbuild-build-depends-bowtie-dummy.deb) ... Processing triggers for install-info ... Setting up libpipeline1 (1.2.0-3) ... Setting up liblocale-gettext-perl (1.05-7) ... Setting up libpcre3 (8.12-4) ... 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 libxml2 (2.7.8.dfsg-4) ... 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 help2man (1.40.4) ... Setting up sbuild-build-depends-bowtie-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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 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 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 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 help2man_1.40.4 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 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 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libffi5_3.0.10~rc10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-10 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-10 libllvm2.9_2.9+dfsg-3 liblocale-gettext-perl_1.05-7 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 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 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 libss2_1.42~WIP-2011-07-02-1 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 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 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 readline-common_6.2-4 sbuild-build-depends-bowtie-dummy_0.invalid.0 sbuild-build-depends-core-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 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_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 Wed Feb 2 13:49:54 2011 CET using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./bowtie_0.12.7-1.dsc dpkg-source: info: extracting bowtie in bowtie-0.12.7 dpkg-source: info: unpacking bowtie_0.12.7.orig.tar.gz dpkg-source: info: unpacking bowtie_0.12.7-1.debian.tar.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 bowtie dpkg-buildpackage: source version 0.12.7-1 dpkg-source --before-build bowtie-0.12.7 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/build/bowtie-aTU5lq/bowtie-0.12.7' rm -f .bowtie* dh_auto_clean make[2]: Entering directory `/build/bowtie-aTU5lq/bowtie-0.12.7' rm -f bowtie-build bowtie bowtie-inspect bowtie-build-debug bowtie-debug bowtie-inspect-debug \ bowtie_prof \ bowtie-build.exe bowtie.exe bowtie-inspect.exe bowtie-build-debug.exe bowtie-debug.exe bowtie-inspect-debug.exe bowtie_prof.exe \ bowtie-src.zip bowtie-bin.zip rm -f core.* make[2]: Leaving directory `/build/bowtie-aTU5lq/bowtie-0.12.7' make[1]: Leaving directory `/build/bowtie-aTU5lq/bowtie-0.12.7' dh_clean dpkg-source -b bowtie-0.12.7 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building bowtie using existing ./bowtie_0.12.7.orig.tar.gz dpkg-source: info: building bowtie in bowtie_0.12.7-1.debian.tar.gz dpkg-source: info: building bowtie in bowtie_0.12.7-1.dsc debian/rules build dh build dh_testdir dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory `/build/bowtie-aTU5lq/bowtie-0.12.7' /usr/bin/make allall make[2]: Entering directory `/build/bowtie-aTU5lq/bowtie-0.12.7' cat ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp aligner.h aligner_0mm.h aligner_1mm.h aligner_23mm.h aligner_metrics.h aligner_seed_mm.h alphabet.h annot.h assert_helpers.h auto_array.h binary_sa_search.h bitpack.h bitset.h blockwise_sa.h color.h color_dec.h diff_sample.h ebwt.h ebwt_search_backtrack.h ebwt_search_util.h edit.h endian_swap.h filebuf.h formats.h hit.h hit_set.h log.h mm.h multikey_qsort.h pat.h pool.h qual.h random_source.h range.h range_cache.h range_chaser.h range_source.h ref_aligner.h ref_read.h reference.h refmap.h row_chaser.h sam.h search_globals.h sequence_io.h shmem.h spinlock.h str_util.h threading.h timer.h tokenize.h word_io.h zbox.h | md5sum | awk '{print $1}' > .bowtie-build.md5 /usr/bin/g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -g -O2 -g -O2 \"" -Wl,--hash-style=both -g -O2 -g -O2 \ -DEBWT_BUILD_HASH=`cat .bowtie-build.md5` \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \ -I SeqAn-1.1 \ -o bowtie-build ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp bowtie_build_main.cpp \ clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated In file included from ebwt_build.cpp:11: ./ebwt.h:1501:1: warning: struct 'SideLocus' was previously declared as a class [-Wmismatched-tags] struct SideLocus { ^~~~~~ class ./ebwt.h:306:7: note: previous use is here class SideLocus; ^ ./ebwt.h:3938:11: error: default arguments cannot be added to an out-of-line definition of a member of a class template uint32_t seed = 0) ^ ~ In file included from ebwt_build.cpp:11: In file included from ./ebwt.h:24: ./alphabet.h:48:3: error: use of undeclared identifier 'reverseInPlace' reverseInPlace(s); ^ In file included from ebwt_build.cpp:11: In file included from ./ebwt.h:31: ./hit.h:97:4: note: in instantiation of function template specialization 'reverseComplementInPlace, seqan::Alloc > >' requested here reverseComplementInPlace(hs.seq, hs.color); ^ 1 warning and 2 errors generated. make[2]: *** [bowtie-build] Error 1 make[2]: Leaving directory `/build/bowtie-aTU5lq/bowtie-0.12.7' make[1]: *** [override_dh_auto_build] Error 2 make[1]: Leaving directory `/build/bowtie-aTU5lq/bowtie-0.12.7' make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20110911-1122 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64c-7e19ce3e-f1a6-4a93-965d-c53f058fbb65/build/bowtie-aTU5lq Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 16232 Build-Time: 4 Distribution: lsid64c Fail-Stage: build Install-Time: 4 Job: bowtie_0.12.7-1 Package: bowtie Package-Time: 18 Source-Version: 0.12.7-1 Space: 16232 Status: attempted Version: 0.12.7-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20110911-1122 Build needed 00:00:18, 16232k disc space DC-Build-Status: Failed 2109.410236s ### Content of /var/log/daemon.log ### Sep 11 10:47:40 talc-104 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:47:51 talc-104 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Sep 11 10:48:32 talc-104 approx: Concurrent download of debian/dists/sid/Release is taking too long Sep 11 10:49:10 talc-104 approx: Concurrent download of debian/dists/sid/main/source/Sources.xz is taking too long ### End of content of /var/log/daemon.log ### DC-Time-Estimation: 2109.410236 versus expected 32000 (r/m: 14.1701169615449 ; m: 2109.410236) DC-Build-Network: USED. See /tmp/rulesafter.RojP2X ! ************************************************************ # Generated by iptables-save v1.4.8 on Sun Sep 11 11:22:55 2011 *filter :INPUT ACCEPT [984931:4234909157] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] [267724:3392354498] -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 [256296:23572169] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT [1220:119452] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT [6:360] -A OUTPUT -j LD [6:360] -A LD -j LOG [6:360] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT # Completed on Sun Sep 11 11:22:55 2011 ************************************************************ --- /tmp/rulesbefore.A1sSj3 2011-09-11 10:47:46.415100359 +0200 +++ /tmp/rulesafter.RojP2X 2011-09-11 11:22:55.831350541 +0200 @@ -1,10 +1,10 @@ -# Generated by iptables-save v1.4.8 on Sun Sep 11 10:47:46 2011 +# Generated by iptables-save v1.4.8 on Sun Sep 11 11:22:55 2011 *filter -:INPUT ACCEPT [341913:794175388] +:INPUT ACCEPT [984931:4234909157] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] -[33063:365149088] -A OUTPUT -o lo -j ACCEPT +[267724:3392354498] -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 -[127694:8029827] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT -[190:21008] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT -[0:0] -A OUTPUT -j LD -[0:0] -A LD -j LOG -[0:0] -A LD -j REJECT --reject-with icmp-port-unreachable +[256296:23572169] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT +[1220:119452] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT +[6:360] -A OUTPUT -j LD +[6:360] -A LD -j LOG +[6:360] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT -# Completed on Sun Sep 11 10:47:46 2011 +# Completed on Sun Sep 11 11:22:55 2011 ************************************************************ [ 11.834120] EDAC MC0: Giving out device to 'i5400_edac.c' 'I5400': DEV 0000:00:10.0 [ 11.834139] EDAC PCI0: Giving out device to module 'i5400_edac' controller 'EDAC PCI controller': DEV '0000:00:10.0' (POLLED) [ 11.835205] ioatdma: Intel(R) QuickData Technology Driver 4.00 [ 11.835257] ioatdma 0000:00:0f.0: PCI INT A -> GSI 16 (level, low) -> IRQ 16 [ 12.084976] [ 12.093988] ioatdma 0000:00:0f.0: setting latency timer to 64 [ 12.094052] alloc irq_desc for 56 on node -1 [ 12.094054] alloc kstat_irqs on node -1 [ 12.094063] ioatdma 0000:00:0f.0: irq 56 for MSI/MSI-X [ 12.094065] alloc irq_desc for 57 on node -1 [ 12.094066] alloc kstat_irqs on node -1 [ 12.094069] ioatdma 0000:00:0f.0: irq 57 for MSI/MSI-X [ 12.094071] alloc irq_desc for 58 on node -1 [ 12.094072] alloc kstat_irqs on node -1 [ 12.094075] ioatdma 0000:00:0f.0: irq 58 for MSI/MSI-X [ 12.094081] alloc irq_desc for 59 on node -1 [ 12.094082] alloc kstat_irqs on node -1 [ 12.094085] ioatdma 0000:00:0f.0: irq 59 for MSI/MSI-X [ 12.094474] processor LNXCPU:05: registered as cooling_device5 [ 12.130124] ACPI: SSDT 00000000bff0134a 0016E (v01 PmRef Cpu6Ist 00003000 INTL 20050228) [ 12.180410] processor LNXCPU:06: registered as cooling_device6 [ 12.215948] ACPI: SSDT 00000000bff014b8 0016E (v01 PmRef Cpu7Ist 00003000 INTL 20050228) [ 12.266272] processor LNXCPU:07: registered as cooling_device7 [ 12.524229] Adding 3911788k swap on /dev/sda1. Priority:-1 extents:1 across:3911788k [ 12.573870] EXT3 FS on sda3, internal journal [ 12.808659] kjournald starting. Commit interval 5 seconds [ 12.808814] EXT3 FS on sda5, internal journal [ 12.808818] EXT3-fs: mounted filesystem with ordered data mode. [ 13.280277] e1000e 0000:0f:00.0: irq 54 for MSI/MSI-X [ 13.336049] e1000e 0000:0f:00.0: irq 54 for MSI/MSI-X [ 13.338228] ADDRCONF(NETDEV_UP): eth0: link is not ready [ 16.383905] e1000e: eth0 NIC Link is Up 1000 Mbps Full Duplex, Flow Control: RX/TX [ 16.433635] ADDRCONF(NETDEV_CHANGE): eth0: link becomes ready [ 26.632004] eth0: no IPv6 routers present [ 420.832593] RPC: Registered udp transport module. [ 420.860860] RPC: Registered tcp transport module. [ 420.889107] RPC: Registered tcp NFSv4.1 backchannel transport module. [ 420.957542] Slow work thread pool: Starting up [ 420.984313] Slow work thread pool: Ready [ 421.007912] FS-Cache: Loaded [ 421.052720] FS-Cache: Netfs 'nfs' registered for caching [ 421.089543] svc: failed to register lockdv1 RPC service (errno 97). [ 452.382084] Adding 296929352k swap on /dev/sda5. Priority:-2 extents:1 across:296929352k [ 469.864304] ip_tables: (C) 2000-2006 Netfilter Core Team [ 1106.743984] IN= OUT=eth0 SRC=172.16.66.104 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=48358 DF PROTO=TCP SPT=48047 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 1109.833015] IN= OUT=eth0 SRC=172.16.66.104 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=48359 DF PROTO=TCP SPT=48047 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2698.120299] IN= OUT=eth0 SRC=172.16.66.104 DST=137.208.57.38 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=29564 DF PROTO=TCP SPT=43641 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2701.208010] IN= OUT=eth0 SRC=172.16.66.104 DST=137.208.57.38 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=29565 DF PROTO=TCP SPT=43641 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2701.578991] IN= OUT=eth0 SRC=172.16.66.104 DST=84.237.118.144 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=45300 DF PROTO=TCP SPT=58667 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2704.669507] IN= OUT=eth0 SRC=172.16.66.104 DST=84.237.118.144 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=45301 DF PROTO=TCP SPT=58667 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 ************************************************************