DC-Build-Header: bwa 0.6.1-1 / Sat Jun 23 16:43:19 +0000 2012 DC-Task: logfile:/tmp/bwa_0.6.1-1_unstable_clang.log version:0.6.1-1 chroot:unstable modes:binary-only:clang source:bwa architecture:any esttime:38 DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang bwa_0.6.1-1' sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on ip-10-28-205-203.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ bwa 0.6.1-1 (amd64) 23 Jun 2012 16:43 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: bwa Version: 0.6.1-1 Source Version: 0.6.1-1 Distribution: unstable Architecture: amd64 I: NOTICE: Log filtering will replace 'build/bwa-hVD5w3/bwa-0.6.1' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/bwa-hVD5w3' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-ff0223f3-49c0-468b-a775-68ba19ff8023' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost unstable InRelease Get:1 http://localhost unstable Release.gpg [836 B] Get:2 http://localhost unstable Release [233 kB] Get:3 http://localhost unstable/main Sources/DiffIndex [7876 B] Get:4 http://localhost unstable/main amd64 Packages/DiffIndex [7876 B] Get:5 http://localhost unstable/main Translation-en/DiffIndex [7876 B] Get:6 http://localhost unstable/main 2012-06-23-0814.36.pdiff [8967 B] Get:7 http://localhost unstable/main 2012-06-23-0814.36.pdiff [8967 B] Get:8 http://localhost unstable/main amd64 2012-06-23-0814.36.pdiff [6101 B] Get:9 http://localhost unstable/main 2012-06-23-0814.36.pdiff [1297 B] Get:10 http://localhost unstable/main amd64 2012-06-23-0814.36.pdiff [6101 B] Get:11 http://localhost unstable/main 2012-06-23-1414.42.pdiff [10.6 kB] Get:12 http://localhost unstable/main 2012-06-23-0814.36.pdiff [1297 B] Get:13 http://localhost unstable/main amd64 2012-06-23-1414.42.pdiff [11.3 kB] Get:14 http://localhost unstable/main 2012-06-23-1414.42.pdiff [10.6 kB] Get:15 http://localhost unstable/main 2012-06-23-1414.42.pdiff [696 B] Get:16 http://localhost unstable/main amd64 2012-06-23-1414.42.pdiff [11.3 kB] Get:17 http://localhost unstable/main 2012-06-23-1414.42.pdiff [696 B] Fetched 296 kB in 7s (41.0 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: base-passwd bsdutils libblkid1 libmount1 libuuid1 mount util-linux 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1300 kB of archives. After this operation, 308 kB disk space will be freed. Get:1 http://localhost/debian/ unstable/main mount amd64 2.20.1-5.1 [213 kB] Get:2 http://localhost/debian/ unstable/main util-linux amd64 2.20.1-5.1 [659 kB] Get:3 http://localhost/debian/ unstable/main base-passwd amd64 3.5.26 [46.3 kB] Get:4 http://localhost/debian/ unstable/main bsdutils amd64 1:2.20.1-5.1 [85.3 kB] Get:5 http://localhost/debian/ unstable/main libuuid1 amd64 2.20.1-5.1 [56.9 kB] Get:6 http://localhost/debian/ unstable/main libblkid1 amd64 2.20.1-5.1 [120 kB] Get:7 http://localhost/debian/ unstable/main libmount1 amd64 2.20.1-5.1 [120 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1300 kB in 0s (13.5 MB/s) (Reading database ... 11730 files and directories currently installed.) Preparing to replace mount 2.20.1-5 (using .../mount_2.20.1-5.1_amd64.deb) ... Unpacking replacement mount ... Setting up mount (2.20.1-5.1) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace util-linux 2.20.1-5 (using .../util-linux_2.20.1-5.1_amd64.deb) ... Unpacking replacement util-linux ... Setting up util-linux (2.20.1-5.1) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace base-passwd 3.5.25 (using .../base-passwd_3.5.26_amd64.deb) ... Unpacking replacement base-passwd ... Setting up base-passwd (3.5.26) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace bsdutils 1:2.20.1-5 (using .../bsdutils_1%3a2.20.1-5.1_amd64.deb) ... Unpacking replacement bsdutils ... Setting up bsdutils (1:2.20.1-5.1) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace libuuid1:amd64 2.20.1-5 (using .../libuuid1_2.20.1-5.1_amd64.deb) ... Unpacking replacement libuuid1:amd64 ... Setting up libuuid1:amd64 (2.20.1-5.1) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace libblkid1:amd64 2.20.1-5 (using .../libblkid1_2.20.1-5.1_amd64.deb) ... Unpacking replacement libblkid1:amd64 ... Setting up libblkid1:amd64 (2.20.1-5.1) ... (Reading database ... 11730 files and directories currently installed.) Preparing to replace libmount1 2.20.1-5 (using .../libmount1_2.20.1-5.1_amd64.deb) ... Unpacking replacement libmount1 ... Setting up libmount1 (2.20.1-5.1) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at: git://git.debian.org/debian-med/bwa.git Need to get 136 kB of source archives. Get:1 http://localhost/debian/ unstable/main bwa 0.6.1-1 (dsc) [1927 B] Get:2 http://localhost/debian/ unstable/main bwa 0.6.1-1 (tar) [130 kB] Get:3 http://localhost/debian/ unstable/main bwa 0.6.1-1 (diff) [4469 B] Fetched 136 kB in 0s (527 kB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/switch-to-clang ──────────────────── + echo 'Entering customization script...' Entering customization script... + apt-get update Ign http://localhost unstable InRelease Hit http://localhost unstable Release.gpg Hit http://localhost unstable Release Hit http://localhost unstable/main Sources/DiffIndex Hit http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Reading package lists... + echo 'Install of clang' Install of clang + apt-get update Ign http://localhost unstable InRelease Hit http://localhost unstable Release.gpg Hit http://localhost unstable Release Hit http://localhost unstable/main Sources/DiffIndex Hit http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Reading package lists... + apt-get install --yes --no-install-recommends clang -t unstable Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libclang-common-dev libffi5 libllvm3.1 Recommended packages: llvm-3.1-dev python The following NEW packages will be installed: clang libclang-common-dev libffi5 libllvm3.1 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 13.1 MB of archives. After this operation, 35.6 MB of additional disk space will be used. Get:1 http://localhost/debian/ unstable/main libffi5 amd64 3.0.10-3 [24.8 kB] Get:2 http://localhost/debian/ unstable/main libllvm3.1 amd64 3.1-1 [7276 kB] Get:3 http://localhost/debian/ unstable/main libclang-common-dev amd64 3.1-6 [84.0 kB] Get:4 http://localhost/debian/ unstable/main clang amd64 3.1-6 [5755 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.1 MB in 0s (29.6 MB/s) Selecting previously unselected package libffi5:amd64. (Reading database ... 11730 files and directories currently installed.) Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ... Selecting previously unselected package libllvm3.1:amd64. Unpacking libllvm3.1:amd64 (from .../libllvm3.1_3.1-1_amd64.deb) ... Selecting previously unselected package libclang-common-dev. Unpacking libclang-common-dev (from .../libclang-common-dev_3.1-6_amd64.deb) ... Selecting previously unselected package clang. Unpacking clang (from .../archives/clang_3.1-6_amd64.deb) ... Setting up libffi5:amd64 (3.0.10-3) ... Setting up libllvm3.1:amd64 (3.1-1) ... Setting up libclang-common-dev (3.1-6) ... Setting up clang (3.1-6) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSION=4.7 + cd /usr/bin + rm g++-4.7 gcc-4.7 cpp-4.7 + ln -s clang++ g++-4.7 + ln -s clang gcc-4.7 + ln -s clang cpp-4.7 + cd - /«BUILDDIR» + echo 'Block the installation of new gcc version' Block the installation of new gcc version + dpkg --set-selections + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'cpp-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'cpp-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + grep clang + gcc --version I: Finished running '/tmp/switch-to-clang'. Finished processing commands. ──────────────────────────────────────────────────────────────────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-1eH2qN/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 debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/706 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 11810 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) ... 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 (>= 8.9.4~), zlib1g-dev 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 (>= 8.9.4~), zlib1g-dev dpkg-deb: building package `sbuild-build-depends-bwa-dummy' in `/«BUILDDIR»/resolver-KRDw2W/apt_archive/sbuild-build-depends-bwa-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install bwa 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 html2text intltool-debian libasprintf0c2 libcroco3 libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less 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 html2text intltool-debian libasprintf0c2 libcroco3 libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-bwa-dummy zlib1g-dev 0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded. Need to get 10.1 MB/10.1 MB of archives. After this operation, 25.8 MB of additional disk space will be used. Get:1 http://localhost/debian/ unstable/main libpipeline1 amd64 1.2.1-1 [39.2 kB] Get:2 http://localhost/debian/ unstable/main libasprintf0c2 amd64 0.18.1.1-9 [26.8 kB] Get:3 http://localhost/debian/ unstable/main libmagic1 amd64 5.11-1 [250 kB] Get:4 http://localhost/debian/ unstable/main libpcre3 amd64 1:8.30-5 [242 kB] Get:5 http://localhost/debian/ unstable/main libxml2 amd64 2.8.0+dfsg1-4 [903 kB] Get:6 http://localhost/debian/ unstable/main libglib2.0-0 amd64 2.32.3-1 [2081 kB] Get:7 http://localhost/debian/ unstable/main libcroco3 amd64 0.6.5-1 [151 kB] Get:8 http://localhost/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB] Get:9 http://localhost/debian/ unstable/main libgettextpo0 amd64 0.18.1.1-9 [145 kB] Get:10 http://localhost/debian/ unstable/main bsdmainutils amd64 9.0.3 [209 kB] Get:11 http://localhost/debian/ unstable/main groff-base amd64 1.21-8 [1152 kB] Get:12 http://localhost/debian/ unstable/main man-db amd64 2.6.2-1 [1061 kB] Get:13 http://localhost/debian/ unstable/main file amd64 5.11-1 [53.2 kB] Get:14 http://localhost/debian/ unstable/main gettext-base amd64 0.18.1.1-9 [154 kB] Get:15 http://localhost/debian/ unstable/main html2text amd64 1.3.2a-15 [103 kB] Get:16 http://localhost/debian/ unstable/main gettext amd64 0.18.1.1-9 [1975 kB] Get:17 http://localhost/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:18 http://localhost/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:19 http://localhost/debian/ unstable/main debhelper all 9.20120608 [700 kB] Get:20 http://localhost/debian/ unstable/main zlib1g-dev amd64 1:1.2.7.dfsg-13 [215 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 10.1 MB in 0s (21.7 MB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... 11810 files and directories currently installed.) Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.1-1_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package libmagic1:amd64. Unpacking libmagic1:amd64 (from .../libmagic1_5.11-1_amd64.deb) ... Selecting previously unselected package libpcre3:amd64. Unpacking libpcre3:amd64 (from .../libpcre3_1%3a8.30-5_amd64.deb) ... Selecting previously unselected package libxml2:amd64. Unpacking libxml2:amd64 (from .../libxml2_2.8.0+dfsg1-4_amd64.deb) ... Selecting previously unselected package libglib2.0-0:amd64. Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.32.3-1_amd64.deb) ... Selecting previously unselected package libcroco3:amd64. Unpacking libcroco3:amd64 (from .../libcroco3_0.6.5-1_amd64.deb) ... Selecting previously unselected package libunistring0:amd64. Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package libgettextpo0:amd64. Unpacking libgettextpo0:amd64 (from .../libgettextpo0_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-8_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.2-1_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.11-1_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ... Selecting previously unselected package zlib1g-dev:amd64. Unpacking zlib1g-dev:amd64 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_amd64.deb) ... Selecting previously unselected package sbuild-build-depends-bwa-dummy. Unpacking sbuild-build-depends-bwa-dummy (from .../sbuild-build-depends-bwa-dummy.deb) ... Setting up libpipeline1:amd64 (1.2.1-1) ... Setting up libasprintf0c2:amd64 (0.18.1.1-9) ... Setting up libmagic1:amd64 (5.11-1) ... Setting up libpcre3:amd64 (1:8.30-5) ... Setting up libxml2:amd64 (2.8.0+dfsg1-4) ... Setting up libglib2.0-0:amd64 (2.32.3-1) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.5-1) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up libgettextpo0:amd64 (0.18.1.1-9) ... Setting up bsdmainutils (9.0.3) ... 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 (1.21-8) ... Setting up man-db (2.6.2-1) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-9) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-9) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120608) ... Setting up zlib1g-dev:amd64 (1:1.2.7.dfsg-13) ... Setting up sbuild-build-depends-bwa-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.22-6.1 dpkg-dev_1.16.4.3 g++-4.6_4.6.3-7 g++-4.7_4.7.1-1 gcc-4.6_4.6.3-7 gcc-4.7_4.7.1-1 libc6-dev_2.13-33 libstdc++6_4.7.1-1 libstdc++6-4.6-dev_4.6.3-7 libstdc++6-4.7-dev_4.7.1-1 linux-libc-dev_3.2.20-1 Package versions: apt_0.9.7 base-files_6.11 base-passwd_3.5.26 bash_4.2-2 binutils_2.22-6.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 clang_3.1-6 coreutils_8.13-3.2 cpp_4:4.7.0-6 cpp-4.6_4.6.3-7 cpp-4.7_4.7.1-1 dash_0.5.7-3 debconf_1.5.44 debconf-i18n_1.5.44 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.1 diffutils_1:3.2-6 dpkg_1.16.4.3 dpkg-dev_1.16.4.3 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-1 findutils_4.4.2-4 g++_4:4.7.0-6 g++-4.6_4.6.3-7 g++-4.7_4.7.1-1 gcc_4:4.7.0-6 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.3-7 gcc-4.6-base_4.6.3-7 gcc-4.7_4.7.1-1 gcc-4.7-base_4.7.1-1 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.12-2 groff-base_1.21-8 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-27 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-33 libc-dev-bin_2.13-33 libc6_2.13-33 libc6-dev_2.13-33 libclang-common-dev_3.1-6 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-4 libdpkg-perl_1.16.4.3 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8 libgcc1_1:4.7.1-1 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-1 libitm1_4.7.1-1 libllvm3.1_3.1-1 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-1 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-9 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libquadmath0_4.7.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-13 libss2_1.42.4-3 libstdc++6_4.7.1-1 libstdc++6-4.6-dev_4.6.3-7 libstdc++6-4.7-dev_4.7.1-1 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-9 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-4 linux-libc-dev_3.2.20-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-33 ncurses-base_5.9-9 ncurses-bin_5.9-9 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 readline-common_6.2-8 sbuild-build-depends-bwa-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-27 sysvinit_2.88dsf-27 sysvinit-utils_2.88dsf-27 tar_1.26-4 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Wed Nov 30 10:45:21 2011 UTC using RSA key ID 2295D502 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./bwa_0.6.1-1.dsc dpkg-source: info: extracting bwa in bwa-0.6.1 dpkg-source: info: unpacking bwa_0.6.1.orig.tar.bz2 dpkg-source: info: unpacking bwa_0.6.1-1.debian.tar.gz Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=root PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/bin/X11 SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=0 SCHROOT_GROUP=root SCHROOT_SESSION_ID=unstable-amd64-sbuild-ff0223f3-49c0-468b-a775-68ba19ff8023 SCHROOT_UID=0 SCHROOT_USER=root SHELL=/bin/sh USER=root dpkg-buildpackage ───────────────── dpkg-buildpackage: warning: using a gain-root-command while being root dpkg-buildpackage: source package bwa dpkg-buildpackage: source version 0.6.1-1 dpkg-buildpackage: source changed by Charles Plessy dpkg-source --before-build bwa-0.6.1 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean make[1]: Entering directory `/«PKGBUILDDIR»' rm -f gmon.out *.o a.out bwa *~ *.a make[1]: Leaving directory `/«PKGBUILDDIR»' dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory `/«PKGBUILDDIR»' dh_auto_build -- CFLAGS="-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro" DFLAGS="-DHAVE_PTHREAD" make[2]: Entering directory `/«PKGBUILDDIR»' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.c -o QSufSort.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' bwt_gen.c:1483:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(bwtInc->textBuffer, sizeof(unsigned char), textSizeInByte, packedFile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwt_gen.c:1452:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(&lastByteLength, sizeof(unsigned char), 1, packedFile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwt_gen.c:1468:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(bwtInc->textBuffer, sizeof(unsigned char), textSizeInByte + 1, packedFile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3 warnings generated. gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD utils.c -o utils.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt.c -o bwt.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtio.c -o bwtio.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' bwtio.c:36:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(&primary, sizeof(bwtint_t), 1, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwtio.c:38:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(skipped, sizeof(bwtint_t), 4, fp); // skip ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwtio.c:39:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(&bwt->sa_intv, sizeof(bwtint_t), 1, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwtio.c:40:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(&primary, sizeof(bwtint_t), 1, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwtio.c:47:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwtio.c:62:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(&bwt->primary, sizeof(bwtint_t), 1, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwtio.c:63:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(bwt->L2+1, sizeof(bwtint_t), 4, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwtio.c:64:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(bwt->bwt, 4, bwt->bwt_size, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 8 warnings generated. gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtaln.c -o bwtaln.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtgap.c -o bwtgap.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD is.c -o is.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bntseq.c -o bntseq.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' bntseq.c:107:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf(fp, "%u%s", &p->gi, str); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ bntseq.c:115:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf(fp, "%lld%d%d", &xx, &p->len, &p->n_ambs); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bntseq.c:99:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf(fp, "%lld%d%u", &xx, &bns->n_seqs, &bns->seed); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bntseq.c:130:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf(fp, "%lld%d%s", &xx, &p->len, str); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bntseq.c:124:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fscanf(fp, "%lld%d%d", &xx, &n_seqs, &bns->n_holes); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5 warnings generated. gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' bwtmisc.c:51:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(&c, 1, 1, fp); ^~~~~ ~~~~~~~~~~~~ bwtmisc.c:72:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(buf2, 1, pac_size, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~ bwtmisc.c:172:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(pac, 1, bns->l_pac/4+1, bns->fp_pac); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3 warnings generated. gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtindex.c -o bwtindex.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD ksw.c -o ksw.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD stdaln.c -o stdaln.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD simple_dp.c -o simple_dp.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwase.c -o bwase.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' bwase.c:308:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(ntpac, 1, ntbns->l_pac/4 + 1, ntbns->fp_pac); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwase.c:314:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(pacseq, 1, bns->l_pac/4+1, bns->fp_pac); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwase.c:617:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(&n_aln, 4, 1, fp_sa); ^~~~~ ~~~~~~~~~~~~~~~~~~~ bwase.c:622:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(aln, sizeof(bwt_aln1_t), n_aln, fp_sa); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwase.c:601:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(&opt, sizeof(gap_opt_t), 1, fp_sa); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5 warnings generated. gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwape.c -o bwape.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' bwape.c:312:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(&n_aln, 4, 1, fp_sa[j]); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~ bwape.c:316:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(d->aln[j].a, sizeof(bwt_aln1_t), n_aln, fp_sa[j]); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwape.c:530:3: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(pacseq, 1, bns->l_pac/4+1, bns->fp_pac); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwape.c:700:4: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(pac, 1, bns->l_pac/4+1, bns->fp_pac); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwape.c:686:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(&opt, sizeof(gap_opt_t), 1, fp_sa[0]); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwape.c:689:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(&opt, sizeof(gap_opt_t), 1, fp_sa[1]); // overwritten! ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 6 warnings generated. gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD kstring.c -o kstring.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD cs2nt.c -o cs2nt.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' bwtsw2_aux.c:758:2: warning: ignoring return value of function declared with warn_unused_result attribute [-Wunused-result] fread(pac, 1, bns->l_pac/4+1, bns->fp_pac); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bamlite.c -o bamlite.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD fastmap.c -o fastmap.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_pair.c -o bwtsw2_pair.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD main.c -o main.o clang: warning: -Wl,-z,relro: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' gcc -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.o bwt_gen.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o ksw.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o fastmap.o bwtsw2_pair.o main.o -o bwa -lm -lz -lpthread clang: warning: argument unused during compilation: '--param ssp-buffer-size=4' bwt.o: In function `bwt_cal_sa': /«PKGBUILDDIR»/bwt.c:71: undefined reference to `bwt_occ' /«PKGBUILDDIR»/bwt.c:71: undefined reference to `bwt_occ' bwt.o: In function `bwt_sa': /«PKGBUILDDIR»/bwt.c:82: undefined reference to `bwt_occ' /«PKGBUILDDIR»/bwt.c:82: undefined reference to `bwt_occ' bwt.o: In function `bwt_match_exact': /«PKGBUILDDIR»/bwt.c:221: undefined reference to `bwt_2occ' bwt.o: In function `bwt_match_exact_alt': /«PKGBUILDDIR»/bwt.c:240: undefined reference to `bwt_2occ' bwt.o: In function `bwt_extend': /«PKGBUILDDIR»/bwt.c:257: undefined reference to `bwt_2occ4' bwtaln.o: In function `bwt_cal_width': /«PKGBUILDDIR»/bwtaln.c:61: undefined reference to `bwt_2occ' bwtgap.o: In function `bwt_match_gap': /«PKGBUILDDIR»/bwtgap.c:194: undefined reference to `bwt_2occ4' bwtsw2_core.o: In function `bsw2_connectivity': /«PKGBUILDDIR»/bwtsw2_core.c:112: undefined reference to `bwtl_2occ4' bwtsw2_core.o: In function `bsw2_core': /«PKGBUILDDIR»/bwtsw2_core.c:494: undefined reference to `bwtl_2occ4' /«PKGBUILDDIR»/bwtsw2_core.c:547: undefined reference to `bwt_2occ4' clang: error: linker command failed with exit code 1 (use -v to see invocation) make[2]: *** [bwa] Error 1 make[2]: Leaving directory `/«PKGBUILDDIR»' dh_auto_build: make -j1 CFLAGS=-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro DFLAGS=-DHAVE_PTHREAD returned exit code 2 make[1]: *** [override_dh_auto_build] Error 2 make[1]: Leaving directory `/«PKGBUILDDIR»' make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120623-1644 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 2144 Build-Time: 8 Distribution: unstable Fail-Stage: build Install-Time: 7 Job: bwa_0.6.1-1 Package: bwa Package-Time: 42 Source-Version: 0.6.1-1 Space: 2144 Status: attempted Version: 0.6.1-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120623-1644 Build needed 00:00:42, 2144k disc space DC-Status: Failed 43.116177s