sbuild (Debian sbuild) 0.63.1 (31 May 2012) on build02.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ bwa 0.6.2-1 (armhf) 07 Jul 2012 00:13 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: bwa Version: 0.6.2-1 Source Version: 0.6.2-1 Distribution: testing Machine Architecture: armhf Host Architecture: armhf Build Architecture: armhf W: line 7 [testing-armhf-sbuild]: Deprecated key ‘script-config’ used I: This option will be removed in the future; please update your configuration I: NOTICE: Log filtering will replace 'build/bwa-5yZipQ/bwa-0.6.2' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/bwa-5yZipQ' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-41e8036a-7ba8-40a2-acb1-654beb46cd13' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Hit http://repo.raspbian.lan testing InRelease Hit http://repo.raspbian.lan testing/main Sources Hit http://repo.raspbian.lan testing/main armhf Packages Ign http://repo.raspbian.lan testing/main Translation-en Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at: git://git.debian.org/debian-med/bwa.git Need to get 135 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main bwa 0.6.2-1 (dsc) [1325 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main bwa 0.6.2-1 (tar) [128 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main bwa 0.6.2-1 (diff) [4827 B] Fetched 135 kB in 0s (2332 kB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-5P36ua/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 1 not upgraded. Need to get 0 B/704 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 ... 10635 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: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), zlib1g-dev Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), zlib1g-dev dpkg-deb: building package `sbuild-build-depends-bwa-dummy' in `/«BUILDDIR»/resolver-wsLCS4/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 libffi5 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 libffi5 libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-bwa-dummy zlib1g-dev debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 22 newly installed, 0 to remove and 1 not upgraded. Need to get 0 B/9670 kB of archives. After this operation, 24.8 MB of additional disk space will be used. Selecting previously unselected package libpcre3:armhf. (Reading database ... 10635 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-5_armhf.deb) ... Selecting previously unselected package libpipeline1:armhf. Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ... Selecting previously unselected package libasprintf0c2:armhf. Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.1.1-9_armhf.deb) ... Selecting previously unselected package libmagic1:armhf. Unpacking libmagic1:armhf (from .../libmagic1_5.11-1_armhf.deb) ... Selecting previously unselected package libxml2:armhf. Unpacking libxml2:armhf (from .../libxml2_2.8.0+dfsg1-4_armhf.deb) ... Selecting previously unselected package libffi5:armhf. Unpacking libffi5:armhf (from .../libffi5_3.0.10-3+b3_armhf.deb) ... Selecting previously unselected package libglib2.0-0:armhf. Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.32.3-1_armhf.deb) ... Selecting previously unselected package libcroco3:armhf. Unpacking libcroco3:armhf (from .../libcroco3_0.6.5-1_armhf.deb) ... Selecting previously unselected package libunistring0:armhf. Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5_armhf.deb) ... Selecting previously unselected package libgettextpo0:armhf. Unpacking libgettextpo0:armhf (from .../libgettextpo0_0.18.1.1-9_armhf.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_armhf.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-9_armhf.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.2-1_armhf.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.11-1_armhf.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_armhf.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_armhf.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-9_armhf.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:armhf. Unpacking zlib1g-dev:armhf (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_armhf.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 libpcre3:armhf (1:8.30-5) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libasprintf0c2:armhf (0.18.1.1-9) ... Setting up libmagic1:armhf (5.11-1) ... Setting up libxml2:armhf (2.8.0+dfsg1-4) ... Setting up libffi5:armhf (3.0.10-3+b3) ... Setting up libglib2.0-0:armhf (2.32.3-1) ... No schema files found: doing nothing. Setting up libcroco3:armhf (0.6.5-1) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up libgettextpo0:armhf (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 (1.21-9) ... 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:armhf (1:1.2.7.dfsg-13) ... Setting up sbuild-build-depends-bwa-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-2-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6.1 dpkg-dev_1.16.4.3 g++-4.6_4.6.3-8+rpi1 gcc-4.6_4.6.3-8+rpi1 libc6-dev_2.13-33 libstdc++6_4.7.1-2+rpi1 libstdc++6-4.6-dev_4.6.3-8+rpi1 linux-libc-dev_3.2.21-1+rpi1 Package versions: apt_0.9.3+rpi1 base-files_6.9 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+b1 bzip2_1.0.6-3 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8+rpi1 dash_0.5.7-3 debconf_1.5.44 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.3 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++_4:4.6.3-6 g++-4.6_4.6.3-8+rpi1 gcc_4:4.6.3-7 gcc-4.4-base_4.4.7-1.1+rpi1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-8+rpi1 gcc-4.6-base_4.6.3-8+rpi1 gcc-4.7-base_4.7.1-2+rpi1 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_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22.1 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.3+rpi1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 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 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+b3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8 libgcc1_1:4.7.1-2+rpi1 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_4.7.1-2+rpi1 liblocale-gettext-perl_1.05-7 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 libncursesw5_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 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_2.2.4-10 libss2_1.42.4-3 libstdc++6_4.7.1-2+rpi1 libstdc++6-4.6-dev_4.6.3-8+rpi1 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-9 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-4 linux-libc-dev_3.2.21-1+rpi1 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+rpi1 perl-base_5.14.2-12+rpi1 perl-modules_5.14.2-12+rpi1 po-debconf_1.0.16+nmu2 raspbian-archive-keyring_20120528.2 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-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 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 Tue Jun 26 07:38:59 2012 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./bwa_0.6.2-1.dsc dpkg-source: info: extracting bwa in bwa-0.6.2 dpkg-source: info: unpacking bwa_0.6.2.orig.tar.bz2 dpkg-source: info: unpacking bwa_0.6.2-1.debian.tar.gz Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=buildd PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/games SCHROOT_ALIAS_NAME=chroot:testing-armhf-sbuild SCHROOT_CHROOT_NAME=testing-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=testing-armhf-sbuild-41e8036a-7ba8-40a2-acb1-654beb46cd13 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package bwa dpkg-buildpackage: source version 0.6.2-1 dpkg-source --before-build bwa-0.6.2 dpkg-buildpackage: host architecture armhf 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 -D_NO_SSE2" 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 -D_NO_SSE2 bwa.c -o bwa.o bwa.c: In function 'bwa_idx_load': bwa.c:52:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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 -D_NO_SSE2 bamlite.c -o bamlite.o 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 -D_NO_SSE2 utils.c -o utils.o 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 -D_NO_SSE2 bwt.c -o bwt.o 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 -D_NO_SSE2 bwtio.c -o bwtio.o bwtio.c: In function 'bwt_restore_bwt': bwtio.c:62:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwtio.c:63:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwtio.c:64:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwtio.c: In function 'bwt_restore_sa': bwtio.c:36:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwtio.c:38:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwtio.c:39:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwtio.c:40:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwtio.c:47:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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 -D_NO_SSE2 bwtaln.c -o bwtaln.o 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 -D_NO_SSE2 bwtgap.c -o bwtgap.o 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 -D_NO_SSE2 bntseq.c -o bntseq.o bntseq.c: In function 'bns_restore_core': bntseq.c:99:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] bntseq.c:107:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] bntseq.c:115:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] bntseq.c:124:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] bntseq.c:130:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] 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 -D_NO_SSE2 stdaln.c -o stdaln.o stdaln.c: In function 'aln_local_core': stdaln.c:545:25: warning: variable 'b' set but not used [-Wunused-but-set-variable] stdaln.c: In function 'aln_extend_core': stdaln.c:865:16: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable] 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 -D_NO_SSE2 bwaseqio.c -o bwaseqio.o 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 -D_NO_SSE2 bwase.c -o bwase.o bwase.c: In function 'bwa_aln2seq_core': bwase.c:74:15: warning: variable 'k' set but not used [-Wunused-but-set-variable] bwase.c: In function 'bwa_print_sam1': bwase.c:445:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable] bwase.c: In function 'bwa_sai2sam_se_core': bwase.c:601:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwase.c:617:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwase.c:622:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwase.c: In function 'bwa_refine_gapped': bwase.c:308:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwase.c:314:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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 -D_NO_SSE2 kstring.c -o kstring.o ar -csru libbwa.a bwa.o bamlite.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o bntseq.o stdaln.o bwaseqio.o bwase.o kstring.o 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 -D_NO_SSE2 QSufSort.c -o QSufSort.o QSufSort.c: In function 'QSufSortSuffixSort': QSufSort.c:62:10: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable] 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 -D_NO_SSE2 bwt_gen.c -o bwt_gen.o bwt_gen.c: In function 'BWTIncBuildRelativeRank': bwt_gen.c:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable] bwt_gen.c: In function 'BWTIncMergeBwt': bwt_gen.c:947:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable] bwt_gen.c: In function 'BWTIncConstructFromPacked': bwt_gen.c:1452:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwt_gen.c:1468:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwt_gen.c:1483:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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 -D_NO_SSE2 is.c -o is.o 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 -D_NO_SSE2 bwtmisc.c -o bwtmisc.o bwtmisc.c: In function 'bwa_pac2cspac_core': bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwtmisc.c: In function 'bwt_pac2bwt': bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwtmisc.c: In function 'bwa_seq_len': bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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 -D_NO_SSE2 bwtindex.c -o bwtindex.o 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 -D_NO_SSE2 ksw.c -o ksw.o 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 -D_NO_SSE2 simple_dp.c -o simple_dp.o 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 -D_NO_SSE2 bwape.c -o bwape.o bwape.c: In function 'bwa_sai2sam_pe_core': bwape.c:686:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwape.c:689:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwape.c:700:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwape.c: In function 'bwa_paired_sw': bwape.c:530:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwape.c: In function 'bwa_cal_pac_pos_pe': bwape.c:312:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] bwape.c:316:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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 -D_NO_SSE2 cs2nt.c -o cs2nt.o 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 -D_NO_SSE2 bwtsw2_core.c -o bwtsw2_core.o 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 -D_NO_SSE2 bwtsw2_main.c -o bwtsw2_main.o 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 -D_NO_SSE2 bwtsw2_aux.c -o bwtsw2_aux.o bwtsw2_aux.c: In function 'gen_cigar': bwtsw2_aux.c:187:7: warning: variable 'score' set but not used [-Wunused-but-set-variable] bwtsw2_aux.c: In function 'bsw2_aln': bwtsw2_aux.c:775:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 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 -D_NO_SSE2 bwt_lite.c -o bwt_lite.o 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 -D_NO_SSE2 bwtsw2_chain.c -o bwtsw2_chain.o 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 -D_NO_SSE2 fastmap.c -o fastmap.o fastmap.c: In function 'main_fastmap': fastmap.c:91:3: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat] 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 -D_NO_SSE2 bwtsw2_pair.c -o bwtsw2_pair.o 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 -D_NO_SSE2 main.c -o main.o gcc -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD -D_NO_SSE2 QSufSort.o bwt_gen.o is.o bwtmisc.o bwtindex.o ksw.o simple_dp.o bwape.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_test -a fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_installcatalogs -a dh_installcron -a dh_installdebconf -a dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_installgsettings -a dh_bugfiles -a dh_ucf -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_usrlocal -a dh_link -a dh_compress -a dh_fixperms -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends} dh_md5sums -a dh_builddeb -a dpkg-deb: building package `bwa' in `../bwa_0.6.2-1_armhf.deb'. dpkg-genchanges -B -mbuildd >../bwa_0.6.2-1_armhf.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build bwa-0.6.2 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120707-0017 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ bwa_0.6.2-1_armhf.changes: ────────────────────────── Format: 1.8 Date: Tue, 26 Jun 2012 09:20:46 +0200 Source: bwa Binary: bwa Architecture: armhf Version: 0.6.2-1 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Andreas Tille Description: bwa - Burrows-Wheeler Aligner Changes: bwa (0.6.2-1) unstable; urgency=low . [ Carlos Borroto ] * New upstream release . [ Andreas Tille ] * debian/control: - versioned Build-Depends debhelper >= 9 - Standards-Version: 3.9.3 (no changes needed) - Add Carlos Borroto as uploader to make sure a package with his changes is not considered as NMU * debian/docs: Add NEWS.Debian * debian/watch: Use SF redirector as suggested by lintian Checksums-Sha1: 1a6bd0718a97ef7e1a9df5dd7879f7f62a081b25 163982 bwa_0.6.2-1_armhf.deb Checksums-Sha256: 0671588e94e99d4074f81c996ef4f030bbe9726b90d4a4fea587c097d84ffc7d 163982 bwa_0.6.2-1_armhf.deb Files: 4a8f6b24b0c7bd3aa38ff60756b0ea74 163982 science optional bwa_0.6.2-1_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ bwa_0.6.2-1_armhf.deb ───────────────────── new debian package, version 2.0. size 163982 bytes: control archive=1032 bytes. 800 bytes, 17 lines control 677 bytes, 11 lines md5sums Package: bwa Version: 0.6.2-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 308 Depends: libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), zlib1g (>= 1:1.1.4) Suggests: samtools Section: science Priority: optional Homepage: http://bio-bwa.sourceforge.net/ Description: Burrows-Wheeler Aligner Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200 bp and the latter for longer sequences up to around 100 kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. drwxr-xr-x root/root 0 2012-07-07 00:17 ./ drwxr-xr-x root/root 0 2012-07-07 00:17 ./usr/ drwxr-xr-x root/root 0 2012-07-07 00:17 ./usr/share/ drwxr-xr-x root/root 0 2012-07-07 00:17 ./usr/share/bwa/ -rwxr-xr-x root/root 616 2012-06-19 10:31 ./usr/share/bwa/qualfa2fq.pl -rwxr-xr-x root/root 730 2012-06-19 10:31 ./usr/share/bwa/xa2multi.pl -rwxr-xr-x root/root 3176 2012-06-19 10:31 ./usr/share/bwa/solid2fastq.pl drwxr-xr-x root/root 0 2012-07-07 00:17 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-07-07 00:17 ./usr/share/doc/bwa/ -rw-r--r-- root/root 17912 2012-06-19 10:31 ./usr/share/doc/bwa/changelog.gz -rw-r--r-- root/root 814 2012-06-19 10:31 ./usr/share/doc/bwa/README -rw-r--r-- root/root 1577 2012-06-26 00:37 ./usr/share/doc/bwa/changelog.Debian.gz -rw-r--r-- root/root 225 2012-06-26 00:37 ./usr/share/doc/bwa/NEWS.Debian.gz -rw-r--r-- root/root 2785 2012-06-26 00:37 ./usr/share/doc/bwa/copyright -rw-r--r-- root/root 7140 2012-06-19 10:31 ./usr/share/doc/bwa/NEWS.gz drwxr-xr-x root/root 0 2012-07-07 00:17 ./usr/share/man/ drwxr-xr-x root/root 0 2012-07-07 00:17 ./usr/share/man/man1/ -rw-r--r-- root/root 7756 2012-07-07 00:17 ./usr/share/man/man1/bwa.1.gz drwxr-xr-x root/root 0 2012-07-07 00:17 ./usr/bin/ -rwxr-xr-x root/root 230868 2012-07-07 00:17 ./usr/bin/bwa ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bsdmainutils* debhelper* file* gettext* gettext-base* groff-base* html2text* intltool-debian* libasprintf0c2* libcroco3* libffi5* libgettextpo0* libglib2.0-0* libmagic1* libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf* sbuild-build-depends-bwa-dummy* sbuild-build-depends-core-dummy* zlib1g-dev* 0 upgraded, 0 newly installed, 23 to remove and 1 not upgraded. After this operation, 24.8 MB disk space will be freed. (Reading database ... 12054 files and directories currently installed.) Removing sbuild-build-depends-bwa-dummy ... Removing debhelper ... Removing man-db ... Purging configuration files for man-db ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing file ... Removing po-debconf ... Removing intltool-debian ... Removing gettext ... Removing gettext-base ... Removing groff-base ... Purging configuration files for groff-base ... Removing html2text ... Purging configuration files for html2text ... Removing libasprintf0c2:armhf ... Removing libcroco3:armhf ... Purging configuration files for libcroco3:armhf ... Removing libglib2.0-0:armhf ... Purging configuration files for libglib2.0-0:armhf ... Removing libffi5:armhf ... Purging configuration files for libffi5:armhf ... Removing libgettextpo0:armhf ... Removing libmagic1:armhf ... Purging configuration files for libmagic1:armhf ... Removing libpcre3:armhf ... Purging configuration files for libpcre3:armhf ... Removing libpipeline1:armhf ... Purging configuration files for libpipeline1:armhf ... Removing libunistring0:armhf ... Purging configuration files for libunistring0:armhf ... Removing libxml2:armhf ... Purging configuration files for libxml2:armhf ... Removing sbuild-build-depends-core-dummy ... Removing zlib1g-dev:armhf ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: armhf Build-Space: 3228 Build-Time: 144 Distribution: testing Host Architecture: armhf Install-Time: 65 Job: bwa_0.6.2-1 Machine Architecture: armhf Package: bwa Package-Time: 228 Source-Version: 0.6.2-1 Space: 3228 Status: successful Version: 0.6.2-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120707-0017 Build needed 00:03:48, 3228k disc space