DC-Build-Header: bowtie2 2.3.1-1 / 2017-07-06 20:24:51 +0000 DC-Task: type:rebuild-binarch-only source:bowtie2 version:2.3.1-1 chroot:unstable esttime:289 logfile:/tmp/bowtie2_2.3.1-1_unstable_clang4.0.log modes:clang40:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang40 bowtie2_2.3.1-1' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-43-7.eu-central-1.compute.internal +==============================================================================+ | bowtie2 2.3.1-1 (amd64) Thu, 06 Jul 2017 20:24:51 +0000 | +==============================================================================+ Package: bowtie2 Version: 2.3.1-1 Source Version: 2.3.1-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-1beb2339-7436-433b-a463-af170f53e00f' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang40 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=4.0 + echo 'Install of clang-4.0' Install of clang-4.0 + apt-get update Hit:1 http://127.0.0.1:9999/debian unstable InRelease Get:2 http://127.0.0.1:9999/debian unstable/main Translation-en [5730 kB] Fetched 5730 kB in 1s (3938 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-4.0 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libbsd0 libclang-common-4.0-dev libclang1-4.0 libedit2 libjsoncpp1 libllvm4.0 libncurses5 libobjc-6-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-4.0-doc libomp-dev Recommended packages: llvm-4.0-dev python libgpm2 The following NEW packages will be installed: clang-4.0 libbsd0 libclang-common-4.0-dev libclang1-4.0 libedit2 libjsoncpp1 libllvm4.0 libncurses5 libobjc-6-dev libobjc4 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 74.4 MB of archives. After this operation, 320 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libbsd0 amd64 0.8.5-1 [89.6 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libncurses5 amd64 6.0+20161126-1 [93.4 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 libedit2 amd64 3.1-20170329-1 [85.2 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libllvm4.0 amd64 1:4.0.1-1 [12.3 MB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-4.0 amd64 1:4.0.1-1 [6355 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libobjc4 amd64 7.1.0-9 [51.0 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libobjc-6-dev amd64 6.4.0-1 [197 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 libclang-common-4.0-dev amd64 1:4.0.1-1 [2495 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 clang-4.0 amd64 1:4.0.1-1 [52.7 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 74.4 MB in 0s (96.5 MB/s) Selecting previously unselected package libbsd0: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 ... 9711 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.8.5-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.5-1) ... Selecting previously unselected package libncurses5:amd64. Preparing to unpack .../1-libncurses5_6.0+20161126-1_amd64.deb ... Unpacking libncurses5:amd64 (6.0+20161126-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../2-libedit2_3.1-20170329-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20170329-1) ... Selecting previously unselected package libllvm4.0:amd64. Preparing to unpack .../3-libllvm4.0_1%3a4.0.1-1_amd64.deb ... Unpacking libllvm4.0:amd64 (1:4.0.1-1) ... Selecting previously unselected package libclang1-4.0:amd64. Preparing to unpack .../4-libclang1-4.0_1%3a4.0.1-1_amd64.deb ... Unpacking libclang1-4.0:amd64 (1:4.0.1-1) ... Selecting previously unselected package libjsoncpp1:amd64. Preparing to unpack .../5-libjsoncpp1_1.7.4-3_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../6-libobjc4_7.1.0-9_amd64.deb ... Unpacking libobjc4:amd64 (7.1.0-9) ... Selecting previously unselected package libobjc-6-dev:amd64. Preparing to unpack .../7-libobjc-6-dev_6.4.0-1_amd64.deb ... Unpacking libobjc-6-dev:amd64 (6.4.0-1) ... Selecting previously unselected package libclang-common-4.0-dev. Preparing to unpack .../8-libclang-common-4.0-dev_1%3a4.0.1-1_amd64.deb ... Unpacking libclang-common-4.0-dev (1:4.0.1-1) ... Selecting previously unselected package clang-4.0. Preparing to unpack .../9-clang-4.0_1%3a4.0.1-1_amd64.deb ... Unpacking clang-4.0 (1:4.0.1-1) ... Setting up libncurses5:amd64 (6.0+20161126-1) ... Setting up libobjc4:amd64 (7.1.0-9) ... Setting up libbsd0:amd64 (0.8.5-1) ... Processing triggers for libc-bin (2.24-12) ... Setting up libobjc-6-dev:amd64 (6.4.0-1) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libedit2:amd64 (3.1-20170329-1) ... Setting up libllvm4.0:amd64 (1:4.0.1-1) ... Setting up libclang1-4.0:amd64 (1:4.0.1-1) ... Setting up libclang-common-4.0-dev (1:4.0.1-1) ... Setting up clang-4.0 (1:4.0.1-1) ... Processing triggers for libc-bin (2.24-12) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-4.0 g++-4.6 + ln -s clang-4.0 gcc-4.6 + ln -s clang-4.0 cpp-4.6 + ln -s clang-4.0 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-4.0 g++-4.7 + ln -s clang-4.0 gcc-4.7 + ln -s clang-4.0 cpp-4.7 + ln -s clang-4.0 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-4.0 g++-4.8 + ln -s clang-4.0 gcc-4.8 + ln -s clang-4.0 cpp-4.8 + ln -s clang-4.0 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-4.0 g++-4.9 + ln -s clang-4.0 gcc-4.9 + ln -s clang-4.0 cpp-4.9 + ln -s clang-4.0 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-4.0 g++-5 + ln -s clang-4.0 gcc-5 + ln -s clang-4.0 cpp-5 + ln -s clang-4.0 gcc + echo 'gcc-5 hold' + dpkg --set-selections + echo 'g++-5 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-4.0 g++-6 + ln -s clang-4.0 gcc-6 + ln -s clang-4.0 cpp-6 + ln -s clang-4.0 gcc + echo 'gcc-6 hold' + dpkg --set-selections + echo 'g++-6 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-7 gcc-7 cpp-7 gcc + ln -s clang++-4.0 g++-7 + ln -s clang-4.0 gcc-7 + ln -s clang-4.0 cpp-7 + ln -s clang-4.0 gcc + echo 'gcc-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + cd - /build/bowtie2-g4neNE + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/clang40'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian unstable InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'bowtie2' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/bowtie2.git Please use: git clone https://anonscm.debian.org/git/debian-med/bowtie2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 5775 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main bowtie2 2.3.1-1 (dsc) [2187 B] Get:2 http://127.0.0.1:9999/debian unstable/main bowtie2 2.3.1-1 (tar) [5761 kB] Get:3 http://127.0.0.1:9999/debian unstable/main bowtie2 2.3.1-1 (diff) [11.9 kB] Fetched 5775 kB in 0s (20.5 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/bowtie2-g4neNE/bowtie2-2.3.1' with '<>' I: NOTICE: Log filtering will replace 'build/bowtie2-g4neNE' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-9xKQx2/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-9xKQx2/apt_archive ./ InRelease Get:2 copy:/<>/resolver-9xKQx2/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-9xKQx2/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-9xKQx2/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-9xKQx2/apt_archive ./ Packages [432 B] Fetched 1738 B in 0s (0 B/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 782 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-9xKQx2/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [782 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 782 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10206 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 kfreebsd-amd64 all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 10), help2man, libtbb-dev, python, liblocal-lib-perl, libtest-deep-perl, libclone-perl, zlib1g-dev, libreadline-dev Filtered Build-Depends: debhelper (>= 10), help2man, libtbb-dev, python, liblocal-lib-perl, libtest-deep-perl, libclone-perl, zlib1g-dev, libreadline-dev dpkg-deb: building package 'sbuild-build-depends-bowtie2-dummy' in '/<>/resolver-9xKQx2/apt_archive/sbuild-build-depends-bowtie2-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-bowtie2-dummy sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-9xKQx2/apt_archive ./ InRelease Get:2 copy:/<>/resolver-9xKQx2/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-9xKQx2/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-9xKQx2/apt_archive ./ Sources [547 B] Get:5 copy:/<>/resolver-9xKQx2/apt_archive ./ Packages [625 B] Fetched 2135 B in 0s (0 B/s) Reading package lists... Reading package lists... Install bowtie2 build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libclone-perl libcroco3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 liblocal-lib-perl liblocale-gettext-perl libmagic-mgc libmagic1 libmodule-build-perl libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline-dev libreadline7 libsigsegv2 libsqlite3-0 libssl1.1 libtbb-dev libtbb2 libtest-deep-perl libtimedate-perl libtinfo-dev libtool libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal readline-common zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff readline-doc tbb-examples libtbb-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libmodule-signature-perl libpod-readme-perl libsoftware-license-perl libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libclone-perl libcroco3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 liblocal-lib-perl liblocale-gettext-perl libmagic-mgc libmagic1 libmodule-build-perl libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline-dev libreadline7 libsigsegv2 libsqlite3-0 libssl1.1 libtbb-dev libtbb2 libtest-deep-perl libtimedate-perl libtinfo-dev libtool libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal readline-common sbuild-build-depends-bowtie2-dummy zlib1g-dev 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 27.1 MB of archives. After this operation, 93.2 MB of additional disk space will be used. Get:1 copy:/<>/resolver-9xKQx2/apt_archive ./ sbuild-build-depends-bowtie2-dummy 0.invalid.0 [840 B] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-9 [1160 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 9.0.12+nmu1 [186 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libpipeline1 amd64 1.4.1-2 [27.6 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 man-db amd64 2.7.6.1-2 [1044 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libpython2.7-minimal amd64 2.7.13-2 [389 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 python2.7-minimal amd64 2.7.13-2 [1383 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 mime-support all 3.60 [36.7 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 libexpat1 amd64 2.2.1-3 [85.6 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 readline-common all 7.0-3 [70.4 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 libsqlite3-0 amd64 3.16.2-5 [572 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 libssl1.1 amd64 1.1.0f-3 [1342 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 libpython2.7-stdlib amd64 2.7.13-2 [1895 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 python2.7 amd64 2.7.13-2 [285 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 python amd64 2.7.13-2 [154 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b1 [18.7 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.30-1 [222 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.30-1 [111 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.30-1 [63.9 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-2+b1 [122 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-6 [7701 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-3 [715 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.11-1 [29.9 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.18-1 [202 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20161112.1 [73.4 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15.1-2 [736 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-2 [433 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:33 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 14 [15.9 kB] Get:34 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:35 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.035-2 [17.0 kB] Get:36 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:37 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.035-2 [10.7 kB] Get:38 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.52.3-1 [2742 kB] Get:39 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.12-1 [144 kB] Get:40 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-2+b1 [1301 kB] Get:41 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:42 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.20 [247 kB] Get:43 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 10.6.2 [968 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 help2man amd64 1.47.4 [162 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 libclone-perl amd64 0.38-2+b1 [13.6 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 libmodule-build-perl all 0.422400-1 [259 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 liblocal-lib-perl all 2.000023-1 [53.5 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 libtinfo-dev amd64 6.0+20161126-1 [78.8 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 libreadline-dev amd64 7.0-3 [132 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 libtbb2 amd64 4.3~20150611-2 [136 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 libtbb-dev amd64 4.3~20150611-2 [236 kB] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 libtest-deep-perl all 1.126-1 [48.4 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-5 [205 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 27.1 MB in 0s (62.4 MB/s) Selecting previously unselected package groff-base. 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Setting up libxml2:amd64 (2.9.4+dfsg1-3) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libmagic1:amd64 (1:5.30-1) ... Setting up libcroco3:amd64 (0.6.12-1) ... Processing triggers for libc-bin (2.24-12) ... Setting up autotools-dev (20161112.1) ... Setting up libssl1.1:amd64 (1.1.0f-3) ... Setting up libreadline-dev:amd64 (7.0-3) ... Setting up libsqlite3-0:amd64 (3.16.2-5) ... Setting up liblocale-gettext-perl (1.07-3+b1) ... Setting up libclone-perl (0.38-2+b1) ... Setting up bsdmainutils (9.0.12+nmu1) ... 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 libmodule-build-perl (0.422400-1) ... Setting up libtbb-dev:amd64 (4.3~20150611-2) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2) ... Setting up autopoint (0.19.8.1-2) ... Setting up liblocal-lib-perl (2.000023-1) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-5) ... Setting up libfile-stripnondeterminism-perl (0.035-2) ... Setting up gettext (0.19.8.1-2+b1) ... Setting up python2.7 (2.7.13-2) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up help2man (1.47.4) ... Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python (2.7.13-2) ... Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.035-2) ... Setting up debhelper (10.6.2) ... Setting up sbuild-build-depends-bowtie2-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-12) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-2-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.28-6 dpkg-dev_1.18.24 g++-6_6.4.0-1 gcc-6_6.4.0-1 libc6-dev_2.24-12 libstdc++-6-dev_6.4.0-1 libstdc++6_7.1.0-9 linux-libc-dev_4.11.6-1 Package versions: adduser_3.115 apt_1.5~beta1 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-6 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-1 build-essential_12.3 bzip2_1.0.6-8.1 clang-4.0_1:4.0.1-1 coreutils_8.26-3 cpp_4:6.3.0-4d1 cpp-6_6.4.0-1 dash_0.5.8-2.4 debconf_1.5.62 debfoster_2.7-2.1+b1 debhelper_10.6.2 debian-archive-keyring_2017.5 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.035-2 diffutils_1:3.5-3 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 eatmydata_105-5 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20170606-2 g++_4:6.3.0-4d1 g++-6_6.4.0-1 gcc_4:6.3.0-4d1 gcc-6_6.4.0-1 gcc-6-base_6.4.0-1 gcc-7-base_7.1.0-9 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gpgv_2.1.18-8 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5+b1 help2man_1.47.4 hostname_3.18+b1 init-system-helpers_1.48 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.5~beta1 libarchive-zip-perl_1.59-1 libasan3_6.4.0-1 libatomic1_7.1.0-9 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 libblkid1_2.29.2-1 libbsd0_0.8.5-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcap-ng0_0.7.7-3+b1 libcc1-0_7.1.0-9 libcilkrts5_7.1.0-9 libclang-common-4.0-dev_1:4.0.1-1 libclang1-4.0_1:4.0.1-1 libclone-perl_0.38-2+b1 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libdb5.3_5.3.28-12+b1 libdebconfclient0_0.229 libdpkg-perl_1.18.24 libeatmydata1_105-5 libedit2_3.1-20170329-1 libexpat1_2.2.1-3 libfakeroot_1.21-3.1 libfdisk1_2.29.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.035-2 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.4.0-1 libgcc1_1:7.1.0-9 libgcrypt20_1.7.8-1 libgdbm3_1.8.3-14 libglib2.0-0_2.52.3-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.13-2 libgomp1_7.1.0-9 libgpg-error0_1.27-3 libhogweed4_3.3-1+b1 libicu57_57.1-6 libidn2-0_0.16-1+b1 libisl15_0.18-1 libitm1_7.1.0-9 libjsoncpp1_1.7.4-3 libllvm4.0_1:4.0.1-1 liblocal-lib-perl_2.000023-1 liblocale-gettext-perl_1.07-3+b1 liblsan0_7.1.0-9 liblz4-1_0.0~r131-2+b1 liblzma5_5.2.2-1.2+b1 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmodule-build-perl_0.422400-1 libmount1_2.29.2-1 libmpc3_1.0.3-1+b2 libmpfr4_3.1.5-1 libmpx2_7.1.0-9 libncurses5_6.0+20161126-1 libncursesw5_6.0+20161126-1 libnettle6_3.3-1+b1 libobjc-6-dev_6.4.0-1 libobjc4_7.1.0-9 libp11-kit0_0.23.7-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-3 libperl5.24_5.24.1-6 libpipeline1_1.4.1-2 libpython-stdlib_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libquadmath0_7.1.0-9 libreadline-dev_7.0-3 libreadline7_7.0-3 libselinux1_2.6-3+b2 libsemanage-common_2.6-2 libsemanage1_2.6-2+b1 libsepol1_2.6-2 libsigsegv2_2.11-1 libsmartcols1_2.29.2-1 libsqlite3-0_3.16.2-5 libss2_1.43.4-2 libssl1.1_1.1.0f-3 libstdc++-6-dev_6.4.0-1 libstdc++6_7.1.0-9 libsystemd0_233-10 libtasn1-6_4.12-2 libtbb-dev_4.3~20150611-2 libtbb2_4.3~20150611-2 libtest-deep-perl_1.126-1 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20161126-1 libtinfo5_6.0+20161126-1 libtool_2.4.6-2 libtsan0_7.1.0-9 libubsan0_7.1.0-9 libudev1_233-10 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-1 libxml2_2.9.4+dfsg1-3 linux-libc-dev_4.11.6-1 login_1:4.4-4.1 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17+b3 mime-support_3.60 mount_2.29.2-1 multiarch-support_2.24-12 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 passwd_1:4.4-4.1 patch_2.7.5-1+b2 perl_5.24.1-6 perl-base_5.24.1-6 perl-modules-5.24_5.24.1-6 po-debconf_1.0.20 python_2.7.13-2 python-minimal_2.7.13-2 python2.7_2.7.13-2 python2.7-minimal_2.7.13-2 readline-common_7.0-3 sbuild-build-depends-bowtie2-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 sysvinit-utils_2.88dsf-59.9 tar_1.29b-1.1 util-linux_2.29.2-1 xz-utils_5.2.2-1.2+b1 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Mar 8 09:31:31 2017 UTC gpgv: using RSA key 1CF792111B5228B0 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bowtie2_2.3.1-1.dsc dpkg-source: info: extracting bowtie2 in /<> dpkg-source: info: unpacking bowtie2_2.3.1.orig.tar.gz dpkg-source: info: unpacking bowtie2_2.3.1-1.debian.tar.xz dpkg-source: info: applying indentation.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying skip_test_requiring_non-free_libmath-random-perl.patch dpkg-source: info: applying do-not-rebuild-during-test.patch dpkg-source: info: applying single-cpu-for-test.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=unstable-amd64-sbuild-1beb2339-7436-433b-a463-af170f53e00f SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package bowtie2 dpkg-buildpackage: info: source version 2.3.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Mestiashvili dpkg-source --before-build bowtie2-2.3.1 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean make -j16 clean make[1]: Entering directory '/<>' 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 rm -rf .perllib.tmp make[1]: Leaving directory '/<>' dh_autoreconf_clean dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- EXTRA_FLAGS="-std=c++98 -Wl,-z,relro -Wl,-z,now" make -j16 "EXTRA_FLAGS=-std=c++98 -Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>' g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -std=c++98 -Wl,-z,relro -Wl,-z,now -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++98 -Wl,-z,relro -Wl,-z,now -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"\"" -DCOMPILER_VERSION="\"\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 diff_sample.cpp bowtie_build_main.cpp \ -lreadline -ltermcap -lz -lpthread -ltbb -ltbbmalloc_proxy -Wl,-z,relro -Wl,-z,now g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -std=c++98 -Wl,-z,relro -Wl,-z,now -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++98 -Wl,-z,relro -Wl,-z,now -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"\"" -DCOMPILER_VERSION="\"\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 diff_sample.cpp bowtie_build_main.cpp \ -lreadline -ltermcap -lz -lpthread -ltbb -ltbbmalloc_proxy -Wl,-z,relro -Wl,-z,now g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -std=c++98 -Wl,-z,relro -Wl,-z,now -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++98 -Wl,-z,relro -Wl,-z,now -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"\"" -DCOMPILER_VERSION="\"\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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 \ -lreadline -ltermcap -lz -lpthread -ltbb -ltbbmalloc_proxy -Wl,-z,relro -Wl,-z,now g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -std=c++98 -Wl,-z,relro -Wl,-z,now -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++98 -Wl,-z,relro -Wl,-z,now -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"\"" -DCOMPILER_VERSION="\"\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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 \ -lreadline -ltermcap -lz -lpthread -ltbb -ltbbmalloc_proxy -Wl,-z,relro -Wl,-z,now g++ -O3 -m64 -msse2 -funroll-loops -g3 \ -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -std=c++98 -Wl,-z,relro -Wl,-z,now -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++98 -Wl,-z,relro -Wl,-z,now -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"\"" -DCOMPILER_VERSION="\"\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 \ -lreadline -ltermcap -lz -lpthread -ltbb -ltbbmalloc_proxy -Wl,-z,relro -Wl,-z,now g++ -O3 -m64 -msse2 -funroll-loops -g3 \ -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -std=c++98 -Wl,-z,relro -Wl,-z,now -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++98 -Wl,-z,relro -Wl,-z,now -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"\"" -DCOMPILER_VERSION="\"\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 \ -lreadline -ltermcap -lz -lpthread -ltbb -ltbbmalloc_proxy -Wl,-z,relro -Wl,-z,now In file included from bt2_build.cpp:27: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from bt2_build.cpp:27: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from bt2_search.cpp:33: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from bt2_search.cpp:33: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from bt2_inspect.cpp:29: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from bt2_inspect.cpp:29: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. 1 warning generated. In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. 1 warning generated. In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. 1 warning generated. 1 warning generated. 1 warning generated. 1 warning generated. 1 warning generated. In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. 1 warning generated. In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. 1 warning generated. 1 warning generated. 1 warning generated. In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. 1 warning generated. In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. 1 warning generated. In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. 1 warning generated. In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. 1 warning generated. In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. In file included from diff_sample.cpp:20: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. In file included from diff_sample.cpp:20: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. In file included from aligner_seed.cpp:23: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from aligner_seed.cpp:23: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. 1 warning generated. In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:103: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:103: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. 1 warning generated. In file included from aligner_sw_driver.cpp:47: In file included from ./aligner_sw_driver.h:84: In file included from ./group_walk.h:86: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ In file included from aligner_sw_driver.cpp:47: In file included from ./aligner_sw_driver.h:84: In file included from ./group_walk.h:86: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:34: ./diff_sample.h:181:37: warning: unknown warning group '-Wmisleading-indentation', ignored [-Wunknown-pragmas] #pragma GCC diagnostic ignored "-Wmisleading-indentation" ^ 1 warning generated. 1 warning generated. aligner_result.cpp:1133:10: error: ordered comparison between pointer and zero ('const char *' and 'int') if(flag > 0) { ~~~~ ^ ~ 1 error generated. Makefile:319: recipe for target 'bowtie2-align-s' failed make[2]: *** [bowtie2-align-s] Error 1 make[2]: *** Waiting for unfinished jobs.... aligner_result.cpp:1133:10: error: ordered comparison between pointer and zero ('const char *' and 'int') if(flag > 0) { ~~~~ ^ ~ 1 error generated. Makefile:327: recipe for target 'bowtie2-align-l' failed make[2]: *** [bowtie2-align-l] Error 1 make[2]: Leaving directory '/<>' dh_auto_build: make -j16 EXTRA_FLAGS=-std=c++98 -Wl,-z,relro -Wl,-z,now returned exit code 2 debian/rules:21: recipe for target 'override_dh_auto_build' failed make[1]: *** [override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>' debian/rules:18: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 2017-07-06T20:25:46Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 28952 Build-Time: 30 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 8 Job: bowtie2_2.3.1-1 Machine Architecture: amd64 Package: bowtie2 Package-Time: 55 Source-Version: 2.3.1-1 Space: 28952 Status: attempted Version: 2.3.1-1 -------------------------------------------------------------------------------- Finished at 2017-07-06T20:25:46Z Build needed 00:00:55, 28952k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 56.163199484s DC-Time-Estimation: 56.163199484 versus expected 289 (r/m: 4.145718239971914 ; m: 56.163199484)