Reading package lists... Building dependency tree... Reading state information... NOTICE: 'bowtie2' packaging is maintained in the 'Git' version control system at: git://anonscm.debian.org/debian-med/bowtie2.git Need to get 3,917 kB of source archives. Get:1 http://urika:3142/ftp.debian.org/debian/ sid/main bowtie2 2.2.5-2 (dsc) [2,146 B] Get:2 http://urika:3142/ftp.debian.org/debian/ sid/main bowtie2 2.2.5-2 (tar) [3,908 kB] Get:3 http://urika:3142/ftp.debian.org/debian/ sid/main bowtie2 2.2.5-2 (diff) [6,816 B] gpgv: keyblock resource `/tmp/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Wed 29 Apr 2015 07:41:28 AM UTC using RSA key ID 1B5228B0 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./bowtie2_2.2.5-2.dsc dpkg-source: info: extracting bowtie2 in bowtie2-2.2.5 dpkg-source: info: unpacking bowtie2_2.2.5.orig.tar.xz dpkg-source: info: unpacking bowtie2_2.2.5-2.debian.tar.xz dpkg-source: info: applying hardening.patch Fetched 3,917 kB in 0s (26.5 MB/s) Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base help2man intltool-debian libasprintf0v5 libcroco3 libexpat1 libffi6 libglib2.0-0 libicu52 libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsqlite3-0 libunistring0 libxml2 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 20.9 MB of archives. After this operation, 74.6 MB of additional disk space will be used. Get:1 http://urika:3142/ftp.debian.org/debian/ sid/main libasprintf0v5 amd64 0.19.5.1-1 [32.2 kB] Get:2 http://urika:3142/ftp.debian.org/debian/ sid/main libmagic1 amd64 1:5.22+15-2 [249 kB] Get:3 http://urika:3142/ftp.debian.org/debian/ sid/main libicu52 amd64 52.1-10 [6,786 kB] Get:4 http://urika:3142/ftp.debian.org/debian/ sid/main libxml2 amd64 2.9.2+dfsg1-3 [934 kB] Get:5 http://urika:3142/ftp.debian.org/debian/ sid/main groff-base amd64 1.22.3-1 [1,205 kB] Get:6 http://urika:3142/ftp.debian.org/debian/ sid/main bsdmainutils amd64 9.0.6 [183 kB] Get:7 http://urika:3142/ftp.debian.org/debian/ sid/main libpipeline1 amd64 1.4.1-1 [27.8 kB] Get:8 http://urika:3142/ftp.debian.org/debian/ sid/main man-db amd64 2.7.2-1 [1,000 kB] Get:9 http://urika:3142/ftp.debian.org/debian/ sid/main libpython2.7-minimal amd64 2.7.10-3 [382 kB] Get:10 http://urika:3142/ftp.debian.org/debian/ sid/main python2.7-minimal amd64 2.7.10-3 [1,418 kB] Get:11 http://urika:3142/ftp.debian.org/debian/ sid/main python-minimal amd64 2.7.9-1 [40.3 kB] Get:12 http://urika:3142/ftp.debian.org/debian/ sid/main mime-support all 3.59 [36.4 kB] Get:13 http://urika:3142/ftp.debian.org/debian/ sid/main libexpat1 amd64 2.1.0-7 [80.0 kB] Get:14 http://urika:3142/ftp.debian.org/debian/ sid/main libffi6 amd64 3.2.1-3 [20.1 kB] Get:15 http://urika:3142/ftp.debian.org/debian/ sid/main libsqlite3-0 amd64 3.8.11.1-1 [454 kB] Get:16 http://urika:3142/ftp.debian.org/debian/ sid/main libpython2.7-stdlib amd64 2.7.10-3 [1,854 kB] Get:17 http://urika:3142/ftp.debian.org/debian/ sid/main python2.7 amd64 2.7.10-3 [258 kB] Get:18 http://urika:3142/ftp.debian.org/debian/ sid/main libpython-stdlib amd64 2.7.9-1 [19.5 kB] Get:19 http://urika:3142/ftp.debian.org/debian/ sid/main python amd64 2.7.9-1 [151 kB] Get:20 http://urika:3142/ftp.debian.org/debian/ sid/main libglib2.0-0 amd64 2.44.1-1.1 [2,461 kB] Get:21 http://urika:3142/ftp.debian.org/debian/ sid/main libcroco3 amd64 0.6.8-3+b1 [135 kB] Get:22 http://urika:3142/ftp.debian.org/debian/ sid/main libunistring0 amd64 0.9.3-5.2+b1 [288 kB] Get:23 http://urika:3142/ftp.debian.org/debian/ sid/main file amd64 1:5.22+15-2 [60.1 kB] Get:24 http://urika:3142/ftp.debian.org/debian/ sid/main gettext-base amd64 0.19.5.1-1 [122 kB] Get:25 http://urika:3142/ftp.debian.org/debian/ sid/main gettext amd64 0.19.5.1-1 [1,459 kB] Get:26 http://urika:3142/ftp.debian.org/debian/ sid/main intltool-debian all 0.35.0+20060710.2 [25.9 kB] Get:27 http://urika:3142/ftp.debian.org/debian/ sid/main po-debconf all 1.0.18 [248 kB] Get:28 http://urika:3142/ftp.debian.org/debian/ sid/main debhelper all 9.20150811 [817 kB] Get:29 http://urika:3142/ftp.debian.org/debian/ sid/main help2man amd64 1.47.1 [150 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 20.9 MB in 0s (55.6 MB/s) Selecting previously unselected package libasprintf0v5:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 15408 files and directories currently installed.) Preparing to unpack .../libasprintf0v5_0.19.5.1-1_amd64.deb ... Unpacking libasprintf0v5:amd64 (0.19.5.1-1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../libmagic1_1%3a5.22+15-2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.22+15-2) ... Selecting previously unselected package libicu52:amd64. Preparing to unpack .../libicu52_52.1-10_amd64.deb ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16807 files and directories currently installed.) Preparing to unpack .../python_2.7.9-1_amd64.deb ... Unpacking python (2.7.9-1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../libglib2.0-0_2.44.1-1.1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.44.1-1.1) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../libcroco3_0.6.8-3+b1_amd64.deb ... 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Setting up libpython2.7-stdlib:amd64 (2.7.10-3) ... Setting up python2.7 (2.7.10-3) ... Setting up libpython-stdlib:amd64 (2.7.9-1) ... Setting up python (2.7.9-1) ... Setting up libglib2.0-0:amd64 (2.44.1-1.1) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.8-3+b1) ... Setting up libunistring0:amd64 (0.9.3-5.2+b1) ... Setting up file (1:5.22+15-2) ... Setting up gettext-base (0.19.5.1-1) ... Setting up gettext (0.19.5.1-1) ... Setting up intltool-debian (0.35.0+20060710.2) ... Setting up po-debconf (1.0.18) ... Setting up debhelper (9.20150811) ... Setting up help2man (1.47.1) ... Processing triggers for libc-bin (2.19-19) ... Killed old client process Internet Systems Consortium DHCP Client 4.3.2 Copyright 2004-2015 Internet Systems Consortium. All rights reserved. For info, please visit https://www.isc.org/software/dhcp/ Listening on LPF/eth0/5e:89:3c:e1:d8:0b Sending on LPF/eth0/5e:89:3c:e1:d8:0b Sending on Socket/fallback DHCPRELEASE on eth0 to 10.0.3.1 port 67 dpkg-buildpackage: source package bowtie2 dpkg-buildpackage: source version 2.2.5-2 dpkg-buildpackage: source distribution unstable dpkg-buildpackage: source changed by Alexandre Mestiashvili dpkg-source --before-build bowtie2-2.2.5 dpkg-buildpackage: host architecture amd64 debian/rules clean dh clean dh_testdir dh_auto_clean make -j1 clean make[1]: Entering directory '/bowtie2-2.2.5' rm -f bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l bowtie2-build-s-debug bowtie2-build-l-debug bowtie2-align-s-debug bowtie2-align-l-debug bowtie2-inspect-s-debug bowtie2-inspect-l-debug \ bowtie2-build-s.exe bowtie2-build-l.exe bowtie2-align-s.exe bowtie2-align-l.exe bowtie2-inspect-s.exe bowtie2-inspect-l.exe bowtie2-build-s-debug.exe bowtie2-build-l-debug.exe bowtie2-align-s-debug.exe bowtie2-align-l-debug.exe bowtie2-inspect-s-debug.exe bowtie2-inspect-l-debug.exe \ bowtie2-src.zip bowtie2-bin.zip rm -f core.* .tmp.head rm -rf *.dSYM make[1]: Leaving directory '/bowtie2-2.2.5' dh_clean dpkg-source -b bowtie2-2.2.5 dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building bowtie2 using existing ./bowtie2_2.2.5.orig.tar.xz dpkg-source: info: building bowtie2 in bowtie2_2.2.5-2.debian.tar.xz dpkg-source: info: building bowtie2 in bowtie2_2.2.5-2.dsc debian/rules build dh build dh_testdir dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/bowtie2-2.2.5' dh_auto_build -- EXTRA_FLAGS=-Wl,-z,relro CPPFLAGS=-D_FORTIFY_SOURCE=2 make -j1 EXTRA_FLAGS=-Wl,-z,relro CPPFLAGS=-D_FORTIFY_SOURCE=2 make[2]: Entering directory '/bowtie2-2.2.5' /usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -Wl,-z,relro\"" -Wl,-z,relro \ -fno-strict-aliasing -DBOWTIE2_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_MM -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -o bowtie2-build-s bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \ -lpthread reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^ /usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -Wl,-z,relro\"" -Wl,-z,relro \ -fno-strict-aliasing -DBOWTIE2_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_MM -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -o bowtie2-build-l bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \ -lpthread reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^ /usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -Wl,-z,relro\"" -Wl,-z,relro \ -fno-strict-aliasing -DBOWTIE2_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_MM -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -o bowtie2-align-s bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -lpthread reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^ /usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -Wl,-z,relro\"" -Wl,-z,relro \ -fno-strict-aliasing -DBOWTIE2_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_MM -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -o bowtie2-align-l bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -lpthread reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^ /usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 \ -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -Wl,-z,relro\"" -Wl,-z,relro \ -fno-strict-aliasing -DBOWTIE2_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_MM -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \ -I third_party -I . \ -o bowtie2-inspect-s bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread /usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 \ -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -Wl,-z,relro\"" -Wl,-z,relro \ -fno-strict-aliasing -DBOWTIE2_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_MM -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -DBOWTIE_64BIT_INDEX -Wall \ -I third_party -I . \ -o bowtie2-inspect-l bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread make[2]: Leaving directory '/bowtie2-2.2.5' make[1]: Leaving directory '/bowtie2-2.2.5' dh_auto_test debian/rules binary dh binary dh_testroot dh_prep dh_installdirs dh_auto_install dh_install dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/bowtie2-2.2.5' dh_installchangelogs NEWS make[1]: Leaving directory '/bowtie2-2.2.5' debian/rules override_dh_installman make[1]: Entering directory '/bowtie2-2.2.5' mkdir -p /bowtie2-2.2.5/debian/bowtie2/usr/share/man/man1/ debian/help2man-wrapper bowtie2 "wrapper for bowtie2-align-*" debian/help2man-wrapper bowtie2-build "wrapper for bowtie2-build-*" debian/help2man-wrapper bowtie2-build-l "building a colorspace index for bowtie2" debian/help2man-wrapper bowtie2-build-s "building a colorspace index for bowtie2" debian/help2man-wrapper bowtie2-inspect "wrapper for bowtie2-inspect-* index" debian/help2man-wrapper bowtie2-inspect-l "extracts information from a bowtie2 index" debian/help2man-wrapper bowtie2-inspect-s "extracts information from a bowtie2 index" debian/help2man-wrapper bowtie2-align-l "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences" debian/help2man-wrapper bowtie2-align-s "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences" rm -f /bowtie2-2.2.5/debian/bowtie2/usr/bin/bowtie2-buildc make[1]: Leaving directory '/bowtie2-2.2.5' dh_perl dh_link dh_compress dh_fixperms dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bowtie2: unused substitution variable ${perl:Depends} dh_md5sums dh_builddeb dpkg-deb: building package 'bowtie2' in '../bowtie2_2.2.5-2_amd64.deb'. dpkg-deb: building package 'bowtie2-examples' in '../bowtie2-examples_2.2.5-2_all.deb'. dpkg-genchanges >../bowtie2_2.2.5-2_amd64.changes dpkg-genchanges: not including original source code in upload dpkg-source --after-build bowtie2-2.2.5 dpkg-buildpackage: binary and diff upload (original source NOT included)