sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build04.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ bowtie 0.12.7-3 (armhf) 05 May 2012 03:29 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: bowtie Version: 0.12.7-3 Source Version: 0.12.7-3 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/bowtie-4LccxD/bowtie-0.12.7' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/bowtie-4LccxD' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-ee5fa6b1-f1cd-4033-813f-78f9e51e3e74' 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 TranslationIndex 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: 'bowtie' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/bowtie/trunk Need to get 7519 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main bowtie 0.12.7-3 (dsc) [1452 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main bowtie 0.12.7-3 (tar) [7511 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main bowtie 0.12.7-3 (diff) [5948 B] Fetched 7519 kB in 0s (9934 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-z5cJT3/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 3 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 ... 10678 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), help2man Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), help2man dpkg-deb: building package `sbuild-build-depends-bowtie-dummy' in `/«BUILDDIR»/resolver-UQhPEY/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 libffi5 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf 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 help2man html2text intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-bowtie-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 20 newly installed, 0 to remove and 3 not upgraded. Need to get 0 B/9444 kB of archives. After this operation, 24.7 MB of additional disk space will be used. Selecting previously unselected package libpcre3:armhf. (Reading database ... 10678 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-4_armhf.deb) ... Selecting previously unselected package libpipeline1:armhf. Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_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_2.7.8.dfsg-9_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_2.32.0-4_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 bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_armhf.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-7_armhf.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.1-2_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_0.18.1.1-5+rpi1_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_0.18.1.1-5+rpi1_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_9.20120419_all.deb) ... Selecting previously unselected package help2man. Unpacking help2man (from .../help2man_1.40.9_armhf.deb) ... Selecting previously unselected package sbuild-build-depends-bowtie-dummy. Unpacking sbuild-build-depends-bowtie-dummy (from .../sbuild-build-depends-bowtie-dummy.deb) ... Setting up libpcre3:armhf (1:8.30-4) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libmagic1:armhf (5.11-1) ... Setting up libxml2:armhf (2.7.8.dfsg-9) ... Setting up libffi5:armhf (3.0.10-3+b3) ... Setting up libglib2.0-0:armhf (2.32.0-4) ... No schema files found: doing nothing. Setting up libcroco3:armhf (0.6.5-1) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up bsdmainutils (9.0.1) ... 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 (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-5+rpi1) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5+rpi1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120419) ... Setting up help2man (1.40.9) ... Setting up sbuild-build-depends-bowtie-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-2-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.2 g++-4.6_4.6.3-1.1+rpi2 gcc-4.6_4.6.3-1.1+rpi2 libc6-dev_2.13-30 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 linux-libc-dev_3.2.12-1 Package versions: apt_0.8.15.10 base-files_6.7 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5+b1 bzip2_1.0.6-1 coreutils_8.13-3.1 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1.1+rpi2 dash_0.5.7-3 debconf_1.5.42 debfoster_2.7-1.1 debhelper_9.20120419 debian-archive-keyring_2010.08.28 debianutils_4.3 diffutils_1:3.2-2 dpkg_1.16.2 dpkg-dev_1.16.2 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.3-1.1+rpi2 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-1.1+rpi2 gcc-4.6-base_4.6.3-1.1+rpi2 gcc-4.7-base_4.7.0-1.1+rpi gettext_0.18.1.1-5+rpi1 gettext-base_0.18.1.1-5+rpi1 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.11-3 groff-base_1.21-7 gzip_1.4-5 help2man_1.40.9 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_2.2.51-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-30 libc-dev-bin_2.13-30 libc6_2.13-30 libc6-dev_2.13-30 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb5.1_5.1.29-1 libdpkg-perl_1.16.2 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgdbm3_1.8.3-10 libglib2.0-0_2.32.0-4 libgmp10_2:5.0.4+dfsg-1 libgomp1_4.7.0-1.1+rpi liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-6 libncursesw5_5.9-6 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_1:8.30-4 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-1 libslang2_2.2.4-7 libss2_1.42.2-2 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 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_5.9-6 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-9 linux-libc-dev_3.2.12-1 login_1:4.1.5-1 lsb-base_4.1+Debian0 make_3.81-8.1 man-db_2.6.1-2 mawk_1.3.3-17 mount_2.20.1-4 multiarch-support_2.13-30 ncurses-base_5.9-6 ncurses-bin_5.9-6 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 po-debconf_1.0.16+nmu2 readline-common_6.2-8 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-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 tzdata_2012b-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Tue Apr 24 11:40:05 2012 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./bowtie_0.12.7-3.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_0.12.7-3.debian.tar.gz dpkg-source: info: applying gcc-4.7.patch dpkg-source: info: applying use-dpkg-buildflags.patch 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_CHROOT_NAME=testing-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=testing-armhf-sbuild-ee5fa6b1-f1cd-4033-813f-78f9e51e3e74 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package bowtie dpkg-buildpackage: source version 0.12.7-3 dpkg-source --before-build bowtie-0.12.7 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/«PKGBUILDDIR»' rm -f .bowtie* dh_auto_clean make[2]: Entering directory `/«PKGBUILDDIR»' 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 `/«PKGBUILDDIR»' 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»' /usr/bin/make allall make[2]: Entering directory `/«PKGBUILDDIR»' 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 -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wl,-z,relro\"" -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wl,-z,relro \ -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 \ In file included from ebwt.h:1603:0, from ebwt_build.cpp:11: ebwt_search_backtrack.h: In member function 'bool GreedyDFSRangeSource::backtrack(uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t*, uint8_t*, bool)': ebwt_search_backtrack.h:770:11: warning: variable 'foundTarget' set but not used [-Wunused-but-set-variable] ebwt_build.cpp: In function 'void driver(const string&, std::vector >&, const string&, bool) [with TStr = seqan::String, seqan::Alloc >, std::string = std::basic_string]': ebwt_build.cpp:589:61: instantiated from here ebwt_build.cpp:344:31: warning: variable 'sztot2' set but not used [-Wunused-but-set-variable] ebwt_build.cpp: In function 'void driver(const string&, std::vector >&, const string&, bool) [with TStr = seqan::String, seqan::Packed<> >, std::string = std::basic_string]': ebwt_build.cpp:600:69: instantiated from here ebwt_build.cpp:344:31: warning: variable 'sztot2' set but not used [-Wunused-but-set-variable] In file included from ebwt_build.cpp:11:0: ebwt.h: In member function 'void Ebwt::buildToDisk(InorderBlockwiseSA&, const TStr&, std::ostream&, std::ostream&) [with TStr = seqan::String, seqan::Alloc >, std::ostream = std::basic_ostream]': ebwt.h:727:5: instantiated from 'void Ebwt::initFromVector(std::vector&, std::vector&, std::vector&, uint32_t, const RefReadInParams&, std::ofstream&, std::ofstream&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t) [with TStr = seqan::String, seqan::Alloc >, uint32_t = unsigned int, std::ofstream = std::basic_ofstream]' ebwt.h:468:3: instantiated from 'Ebwt::Ebwt(int, int32_t, int32_t, int32_t, int32_t, int32_t, const string&, bool, bool, uint32_t, uint32_t, uint32_t, int, std::vector&, std::vector&, std::vector&, uint32_t, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool) [with TStr = seqan::String, seqan::Alloc >, int32_t = int, std::string = std::basic_string, uint32_t = unsigned int]' ebwt_build.cpp:439:29: instantiated from 'void driver(const string&, std::vector >&, const string&, bool) [with TStr = seqan::String, seqan::Alloc >, std::string = std::basic_string]' ebwt_build.cpp:589:61: instantiated from here ebwt.h:4191:7: warning: variable 'wroteFwBucket' set but not used [-Wunused-but-set-variable] In file included from ebwt_build.cpp:11:0: ebwt.h: In member function 'void Ebwt::sanityCheckUpToSide(int) const [with TStr = seqan::String, seqan::Alloc >]': ebwt.h:1763:2: instantiated from 'void Ebwt::sanityCheckAll(int) const [with TStr = seqan::String, seqan::Alloc >]' ebwt.h:519:4: instantiated from 'Ebwt::Ebwt(int, int32_t, int32_t, int32_t, int32_t, int32_t, const string&, bool, bool, uint32_t, uint32_t, uint32_t, int, std::vector&, std::vector&, std::vector&, uint32_t, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool) [with TStr = seqan::String, seqan::Alloc >, int32_t = int, std::string = std::basic_string, uint32_t = unsigned int]' ebwt_build.cpp:439:29: instantiated from 'void driver(const string&, std::vector >&, const string&, bool) [with TStr = seqan::String, seqan::Alloc >, std::string = std::basic_string]' ebwt_build.cpp:589:61: instantiated from here ebwt.h:1667:11: warning: variable 'occ_save' set but not used [-Wunused-but-set-variable] In file included from ebwt_build.cpp:11:0: ebwt.h: In member function 'void Ebwt::buildToDisk(InorderBlockwiseSA&, const TStr&, std::ostream&, std::ostream&) [with TStr = seqan::String, seqan::Packed<> >, std::ostream = std::basic_ostream]': ebwt.h:727:5: instantiated from 'void Ebwt::initFromVector(std::vector&, std::vector&, std::vector&, uint32_t, const RefReadInParams&, std::ofstream&, std::ofstream&, bool, uint32_t, uint32_t, uint32_t, int, uint32_t) [with TStr = seqan::String, seqan::Packed<> >, uint32_t = unsigned int, std::ofstream = std::basic_ofstream]' ebwt.h:468:3: instantiated from 'Ebwt::Ebwt(int, int32_t, int32_t, int32_t, int32_t, int32_t, const string&, bool, bool, uint32_t, uint32_t, uint32_t, int, std::vector&, std::vector&, std::vector&, uint32_t, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool) [with TStr = seqan::String, seqan::Packed<> >, int32_t = int, std::string = std::basic_string, uint32_t = unsigned int]' ebwt_build.cpp:439:29: instantiated from 'void driver(const string&, std::vector >&, const string&, bool) [with TStr = seqan::String, seqan::Packed<> >, std::string = std::basic_string]' ebwt_build.cpp:600:69: instantiated from here ebwt.h:4191:7: warning: variable 'wroteFwBucket' set but not used [-Wunused-but-set-variable] In file included from ebwt_build.cpp:11:0: ebwt.h: In member function 'void Ebwt::sanityCheckUpToSide(int) const [with TStr = seqan::String, seqan::Packed<> >]': ebwt.h:1763:2: instantiated from 'void Ebwt::sanityCheckAll(int) const [with TStr = seqan::String, seqan::Packed<> >]' ebwt.h:519:4: instantiated from 'Ebwt::Ebwt(int, int32_t, int32_t, int32_t, int32_t, int32_t, const string&, bool, bool, uint32_t, uint32_t, uint32_t, int, std::vector&, std::vector&, std::vector&, uint32_t, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool) [with TStr = seqan::String, seqan::Packed<> >, int32_t = int, std::string = std::basic_string, uint32_t = unsigned int]' ebwt_build.cpp:439:29: instantiated from 'void driver(const string&, std::vector >&, const string&, bool) [with TStr = seqan::String, seqan::Packed<> >, std::string = std::basic_string]' ebwt_build.cpp:600:69: instantiated from here ebwt.h:1667:11: warning: variable 'occ_save' set but not used [-Wunused-but-set-variable] ref_read.cpp: In function 'void reverseRefRecords(const std::vector&, std::vector&, bool, bool)': ref_read.cpp:195:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable] ref_read.cpp: In function 'std::pair fastaRefReadSizes(std::vector&, std::vector&, std::vector&, const RefReadInParams&, BitpairOutFileBuf*, int&)': ref_read.cpp:243:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable] cat ebwt_search.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.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 search_1mm_phase1.c search_1mm_phase2.c search_23mm_phase1.c search_23mm_phase2.c search_23mm_phase3.c search_seeded_phase1.c search_seeded_phase2.c search_seeded_phase3.c search_seeded_phase4.c | md5sum | awk '{print $1}' > .bowtie.md5 /usr/bin/g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wl,-z,relro\"" -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wl,-z,relro \ -DEBWT_SEARCH_HASH=`cat .bowtie.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 ebwt_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \ -lpthread In file included from ebwt.h:1603:0, from ebwt_search.cpp:15: ebwt_search_backtrack.h: In member function 'bool GreedyDFSRangeSource::backtrack(uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t*, uint8_t*, bool)': ebwt_search_backtrack.h:770:11: warning: variable 'foundTarget' set but not used [-Wunused-but-set-variable] In file included from ebwt_search.cpp:1895:0: search_23mm_phase3.c: In function 'void* twoOrThreeMismatchSearchWorkerFull(void*)': search_23mm_phase3.c:27:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable] search_23mm_phase3.c:48:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable] In file included from ebwt_search.cpp:2164:0: search_seeded_phase3.c: In function 'void* seededQualSearchWorkerFull(void*)': search_seeded_phase3.c:64:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable] In file included from ebwt_search.cpp:2165:0: search_seeded_phase4.c:66:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable] ref_read.cpp: In function 'void reverseRefRecords(const std::vector&, std::vector&, bool, bool)': ref_read.cpp:195:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable] ref_read.cpp: In function 'std::pair fastaRefReadSizes(std::vector&, std::vector&, std::vector&, const RefReadInParams&, BitpairOutFileBuf*, int&)': ref_read.cpp:243:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable] sam.cpp: In static member function 'static void SAMHitSink::appendAligned(std::ostream&, const Hit&, int, int, const std::vector >*, ReferenceMap*, AnnotationMap*, bool, int)': sam.cpp:150:22: warning: variable 'pat' set but not used [-Wunused-but-set-variable] color_dec.cpp: In function 'void decodeHit(const char*, const char*, size_t, size_t, const char*, size_t, size_t, int, char*, char*, char*, int&, int&)': color_dec.cpp:187:6: warning: variable 'lastOmin' set but not used [-Wunused-but-set-variable] cat bowtie_inspect.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 ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp | md5sum | awk '{print $1}' > .bowtie-inspect.md5 /usr/bin/g++ -O3 \ -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wl,-z,relro\"" -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wl,-z,relro \ -DEBWT_INSPECT_HASH=`cat .bowtie-inspect.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 -Wall \ -I SeqAn-1.1 -I . \ -o bowtie-inspect bowtie_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp \ ref_read.cpp: In function 'void reverseRefRecords(const std::vector&, std::vector&, bool, bool)': ref_read.cpp:195:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable] ref_read.cpp: In function 'std::pair fastaRefReadSizes(std::vector&, std::vector&, std::vector&, const RefReadInParams&, BitpairOutFileBuf*, int&)': ref_read.cpp:243:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable] 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-debug.md5 /usr/bin/g++ -O0 -g3 -DCOMPILER_OPTIONS="\"-O0 -g3 -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wl,-z,relro\"" -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wl,-z,relro \ -DEBWT_BUILD_HASH=`cat .bowtie-build-debug.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 -Wall \ -I SeqAn-1.1 \ -o bowtie-build-debug ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp bowtie_build_main.cpp \ ebwt_build.cpp: In function 'void driver(const string&, std::vector >&, const string&, bool) [with TStr = seqan::String, seqan::Alloc >, std::string = std::basic_string]': ebwt_build.cpp:589:61: instantiated from here ebwt_build.cpp:344:31: warning: variable 'sztot2' set but not used [-Wunused-but-set-variable] ebwt_build.cpp:401:31: warning: variable 'sztot2' set but not used [-Wunused-but-set-variable] ebwt_build.cpp: In function 'void driver(const string&, std::vector >&, const string&, bool) [with TStr = seqan::String, seqan::Packed<> >, std::string = std::basic_string]': ebwt_build.cpp:600:69: instantiated from here ebwt_build.cpp:344:31: warning: variable 'sztot2' set but not used [-Wunused-but-set-variable] ebwt_build.cpp:401:31: warning: variable 'sztot2' set but not used [-Wunused-but-set-variable] ref_read.cpp: In function 'void reverseRefRecords(const std::vector&, std::vector&, bool, bool)': ref_read.cpp:195:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable] ref_read.cpp: In function 'std::pair fastaRefReadSizes(std::vector&, std::vector&, std::vector&, const RefReadInParams&, BitpairOutFileBuf*, int&)': ref_read.cpp:243:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable] cat ebwt_search.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.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 search_1mm_phase1.c search_1mm_phase2.c search_23mm_phase1.c search_23mm_phase2.c search_23mm_phase3.c search_seeded_phase1.c search_seeded_phase2.c search_seeded_phase3.c search_seeded_phase4.c | md5sum | awk '{print $1}' > .bowtie-debug.md5 /usr/bin/g++ -O0 -g3 \ -DCOMPILER_OPTIONS="\"-O0 -g3 -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wl,-z,relro\"" -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wl,-z,relro \ -DEBWT_SEARCH_HASH=`cat .bowtie-debug.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 -Wall \ -I SeqAn-1.1 \ -o bowtie-debug ebwt_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \ -lpthread In file included from ebwt_search.cpp:1895:0: search_23mm_phase3.c: In function 'void* twoOrThreeMismatchSearchWorkerFull(void*)': search_23mm_phase3.c:27:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable] search_23mm_phase3.c:48:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable] In file included from ebwt_search.cpp:2164:0: search_seeded_phase3.c: In function 'void* seededQualSearchWorkerFull(void*)': search_seeded_phase3.c:64:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable] In file included from ebwt_search.cpp:2165:0: search_seeded_phase4.c:66:8: warning: variable 'gaveUp' set but not used [-Wunused-but-set-variable] ref_read.cpp: In function 'void reverseRefRecords(const std::vector&, std::vector&, bool, bool)': ref_read.cpp:195:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable] ref_read.cpp: In function 'std::pair fastaRefReadSizes(std::vector&, std::vector&, std::vector&, const RefReadInParams&, BitpairOutFileBuf*, int&)': ref_read.cpp:243:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable] color_dec.cpp: In function 'void decodeHit(const char*, const char*, size_t, size_t, const char*, size_t, size_t, int, char*, char*, char*, int&, int&)': color_dec.cpp:187:6: warning: variable 'lastOmin' set but not used [-Wunused-but-set-variable] cat bowtie_inspect.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 ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp | md5sum | awk '{print $1}' > .bowtie-inspect-debug.md5 /usr/bin/g++ -O0 -g3 \ -DCOMPILER_OPTIONS="\"-O0 -g3 -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wl,-z,relro\"" -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wl,-z,relro \ -DEBWT_INSPECT_HASH=`cat .bowtie-inspect-debug.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 -Wall \ -I SeqAn-1.1 -I . \ -o bowtie-inspect-debug bowtie_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp \ ref_read.cpp: In function 'void reverseRefRecords(const std::vector&, std::vector&, bool, bool)': ref_read.cpp:195:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable] ref_read.cpp: In function 'std::pair fastaRefReadSizes(std::vector&, std::vector&, std::vector&, const RefReadInParams&, BitpairOutFileBuf*, int&)': ref_read.cpp:243:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable] 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 debian/rules override_dh_auto_install make[1]: Entering directory `/«PKGBUILDDIR»' help2man --name="ultrafast memory-efficient short read aligner" --no-info \ /«PKGBUILDDIR»/bowtie > /«PKGBUILDDIR»/debian/bowtie/usr/share/man/man1/bowtie.1 help2man --name="building a colorspace index for bowtie" --no-info \ /«PKGBUILDDIR»/bowtie-build > /«PKGBUILDDIR»/debian/bowtie/usr/share/man/man1/bowtie-build.1 help2man --name="extracts information from a bowtie index" --no-info \ /«PKGBUILDDIR»/bowtie-inspect > /«PKGBUILDDIR»/debian/bowtie/usr/share/man/man1/bowtie-inspect.1 make[1]: Leaving directory `/«PKGBUILDDIR»' 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 dpkg-shlibdeps: warning: debian/bowtie/usr/bin/bowtie-build contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/bowtie/usr/bin/bowtie-debug contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/bowtie/usr/bin/bowtie contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/bowtie/usr/bin/bowtie-inspect contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/bowtie/usr/bin/bowtie-inspect-debug contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: debian/bowtie/usr/bin/bowtie-build-debug contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package `bowtie' in `../bowtie_0.12.7-3_armhf.deb'. dpkg-genchanges -B -mbuildd >../bowtie_0.12.7-3_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 bowtie-0.12.7 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120505-0409 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ bowtie_0.12.7-3_armhf.changes: ────────────────────────────── Format: 1.8 Date: Tue, 24 Apr 2012 13:21:32 +0200 Source: bowtie Binary: bowtie bowtie-examples Architecture: armhf Version: 0.12.7-3 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Andreas Tille Description: bowtie - ultrafast memory-efficient short read aligner bowtie-examples - Examples for bowtie, the ultrafast memory-efficient short read al Closes: 670230 Changes: bowtie (0.12.7-3) unstable; urgency=low . * debian/patches/use-dpkg-buildflags.patch: Regard LDFLAGS/CPPFLAGS hardening flags (thanks for the patch to Simon Ruderich ) Closes: #670230 Checksums-Sha1: dcee84f88a87596dce4750ab47673d54098bd25f 1294834 bowtie_0.12.7-3_armhf.deb Checksums-Sha256: 0d31d5bd4b910b580795d7ba763d27771a4508f84cf712b2f36aeef6c058d953 1294834 bowtie_0.12.7-3_armhf.deb Files: 37caac8aa8f193ee65da035236b4cdc6 1294834 science extra bowtie_0.12.7-3_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ bowtie_0.12.7-3_armhf.deb ───────────────────────── new debian package, version 2.0. size 1294834 bytes: control archive= 1294 bytes. 997 bytes, 21 lines control 1076 bytes, 17 lines md5sums Package: bowtie Version: 0.12.7-3 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 2739 Depends: libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0) Suggests: bowtie-examples Section: science Priority: extra Homepage: http://bowtie-bio.sourceforge.net/ Description: ultrafast memory-efficient short read aligner This package addresses the problem to interpret the results from the latest (2010) DNA sequencing technologies. Those will yield fairly short stretches and those cannot be interpreted directly. It is the challenge for tools like Bowtie to give a chromosomal location to the short stretches of DNA sequenced per run. . Bowtie aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end). drwxr-xr-x root/root 0 2012-05-05 04:08 ./ drwxr-xr-x root/root 0 2012-05-05 04:08 ./usr/ drwxr-xr-x root/root 0 2012-05-05 04:08 ./usr/bin/ -rwxr-xr-x root/root 220108 2012-05-05 04:08 ./usr/bin/bowtie-build -rwxr-xr-x root/root 506468 2012-05-05 04:08 ./usr/bin/bowtie -rwxr-xr-x root/root 1063552 2012-05-05 04:08 ./usr/bin/bowtie-debug -rwxr-xr-x root/root 168100 2012-05-05 04:08 ./usr/bin/bowtie-inspect -rwxr-xr-x root/root 470016 2012-05-05 04:08 ./usr/bin/bowtie-build-debug -rwxr-xr-x root/root 168100 2012-05-05 04:08 ./usr/bin/bowtie-inspect-debug drwxr-xr-x root/root 0 2012-05-05 04:08 ./usr/share/ drwxr-xr-x root/root 0 2012-05-05 04:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-05 04:08 ./usr/share/doc/bowtie/ -rw-r--r-- root/root 10825 2010-09-07 13:47 ./usr/share/doc/bowtie/NEWS.gz -rw-r--r-- root/root 119040 2010-09-07 13:55 ./usr/share/doc/bowtie/manual.html -rw-r--r-- root/root 652 2012-04-24 04:34 ./usr/share/doc/bowtie/changelog.Debian.gz -rw-r--r-- root/root 4182 2009-12-16 15:00 ./usr/share/doc/bowtie/style.css -rw-r--r-- root/root 2576 2009-10-05 14:55 ./usr/share/doc/bowtie/TUTORIAL.gz -rw-r--r-- root/root 21349 2010-09-07 13:54 ./usr/share/doc/bowtie/MANUAL.gz -rw-r--r-- root/root 2543 2012-04-23 03:31 ./usr/share/doc/bowtie/copyright drwxr-xr-x root/root 0 2012-05-05 04:08 ./usr/share/doc-base/ -rw-r--r-- root/root 1010 2011-01-30 06:24 ./usr/share/doc-base/bowtie drwxr-xr-x root/root 0 2012-05-05 04:08 ./usr/share/man/ drwxr-xr-x root/root 0 2012-05-05 04:08 ./usr/share/man/man1/ -rw-r--r-- root/root 894 2012-05-05 04:08 ./usr/share/man/man1/bowtie-inspect.1.gz -rw-r--r-- root/root 1151 2012-05-05 04:08 ./usr/share/man/man1/bowtie-build.1.gz -rw-r--r-- root/root 2652 2012-05-05 04:08 ./usr/share/man/man1/bowtie.1.gz lrwxrwxrwx root/root 0 2012-05-05 04:08 ./usr/share/man/man1/bowtie-debug.1.gz -> bowtie.1.gz lrwxrwxrwx root/root 0 2012-05-05 04:08 ./usr/share/man/man1/bowtie-build-debug.1.gz -> bowtie-build.1.gz lrwxrwxrwx root/root 0 2012-05-05 04:08 ./usr/share/man/man1/bowtie-inspect-debug.1.gz -> bowtie-inspect.1.gz ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 3 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* help2man* html2text* intltool-debian* libcroco3* libffi5* libglib2.0-0* libmagic1* libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf* sbuild-build-depends-bowtie-dummy* sbuild-build-depends-core-dummy* 0 upgraded, 0 newly installed, 21 to remove and 3 not upgraded. After this operation, 24.7 MB disk space will be freed. (Reading database ... 12109 files and directories currently installed.) Removing sbuild-build-depends-bowtie-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 help2man ... Removing html2text ... Purging configuration files for html2text ... 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 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 ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 44552 Build-Time: 2303 Distribution: testing Install-Time: 52 Job: bowtie_0.12.7-3 Package: bowtie Package-Time: 2373 Source-Version: 0.12.7-3 Space: 44552 Status: successful Version: 0.12.7-3 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120505-0409 Build needed 00:39:33, 44552k disc space