DC-Build-Header: tophat 2.1.1+dfsg-2 / 2017-07-06 19:33:30 +0000 DC-Task: type:rebuild-binarch-only source:tophat version:2.1.1+dfsg-2 chroot:unstable esttime:477 logfile:/tmp/tophat_2.1.1+dfsg-2_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 tophat_2.1.1+dfsg-2' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-38-0.eu-central-1.compute.internal +==============================================================================+ | tophat 2.1.1+dfsg-2 (amd64) Thu, 06 Jul 2017 19:33:30 +0000 | +==============================================================================+ Package: tophat Version: 2.1.1+dfsg-2 Source Version: 2.1.1+dfsg-2 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-3fafb28c-7d87-4f94-9ea8-c26c3b375b52' 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 (3969 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 (95.8 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/tophat-5F5urv + 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: 'tophat' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/tophat.git Please use: git clone https://anonscm.debian.org/git/debian-med/tophat.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 564 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main tophat 2.1.1+dfsg-2 (dsc) [2187 B] Get:2 http://127.0.0.1:9999/debian unstable/main tophat 2.1.1+dfsg-2 (tar) [554 kB] Get:3 http://127.0.0.1:9999/debian unstable/main tophat 2.1.1+dfsg-2 (diff) [7276 B] Fetched 564 kB in 0s (2620 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/tophat-5F5urv/tophat-2.1.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/tophat-5F5urv' 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-SFoqpr/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-SFoqpr/apt_archive ./ InRelease Get:2 copy:/<>/resolver-SFoqpr/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-SFoqpr/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-SFoqpr/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-SFoqpr/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-SFoqpr/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) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 9), autotools-dev, libbam-dev, zlib1g-dev, dh-autoreconf, python, seqan-dev (>= 1.4), libboost-system-dev, libboost-thread-dev, help2man Filtered Build-Depends: debhelper (>= 9), autotools-dev, libbam-dev, zlib1g-dev, dh-autoreconf, python, seqan-dev (>= 1.4), libboost-system-dev, libboost-thread-dev, help2man dpkg-deb: building package 'sbuild-build-depends-tophat-dummy' in '/<>/resolver-SFoqpr/apt_archive/sbuild-build-depends-tophat-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-tophat-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-SFoqpr/apt_archive ./ InRelease Get:2 copy:/<>/resolver-SFoqpr/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-SFoqpr/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-SFoqpr/apt_archive ./ Sources [557 B] Get:5 copy:/<>/resolver-SFoqpr/apt_archive ./ Packages [633 B] Fetched 2153 B in 0s (0 B/s) Reading package lists... Reading package lists... Install tophat 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 libbam-dev libboost-atomic1.62-dev libboost-atomic1.62.0 libboost-chrono1.62-dev libboost-chrono1.62.0 libboost-date-time1.62-dev libboost-date-time1.62.0 libboost-serialization1.62-dev libboost-serialization1.62.0 libboost-system-dev libboost-system1.62-dev libboost-system1.62.0 libboost-thread-dev libboost-thread1.62-dev libboost-thread1.62.0 libboost1.62-dev libcroco3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 libsigsegv2 libsqlite3-0 libssl1.1 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal readline-common seqan-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost1.62-doc libboost-context1.62-dev libboost-coroutine1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev libboost-filesystem1.62-dev libboost-graph1.62-dev libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev libboost-program-options1.62-dev libboost-python1.62-dev libboost-random1.62-dev libboost-regex1.62-dev libboost-signals1.62-dev libboost-test1.62-dev libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev libboost1.62-tools-dev libmpfrc++-dev libntl-dev libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs 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 libbam-dev libboost-atomic1.62-dev libboost-atomic1.62.0 libboost-chrono1.62-dev libboost-chrono1.62.0 libboost-date-time1.62-dev libboost-date-time1.62.0 libboost-serialization1.62-dev libboost-serialization1.62.0 libboost-system-dev libboost-system1.62-dev libboost-system1.62.0 libboost-thread-dev libboost-thread1.62-dev libboost-thread1.62.0 libboost1.62-dev libcroco3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 libsigsegv2 libsqlite3-0 libssl1.1 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal readline-common sbuild-build-depends-tophat-dummy seqan-dev zlib1g-dev 0 upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 35.1 MB of archives. After this operation, 221 MB of additional disk space will be used. Get:1 copy:/<>/resolver-SFoqpr/apt_archive ./ sbuild-build-depends-tophat-dummy 0.invalid.0 [852 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 libbam-dev amd64 0.1.19-2 [123 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 libboost1.62-dev amd64 1.62.0+dfsg-4+b1 [7053 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 libboost-atomic1.62.0 amd64 1.62.0+dfsg-4+b1 [30.8 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 libboost-atomic1.62-dev amd64 1.62.0+dfsg-4+b1 [29.7 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 libboost-system1.62.0 amd64 1.62.0+dfsg-4+b1 [32.7 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 libboost-chrono1.62.0 amd64 1.62.0+dfsg-4+b1 [36.3 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 libboost-chrono1.62-dev amd64 1.62.0+dfsg-4+b1 [36.7 kB] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 libboost-date-time1.62.0 amd64 1.62.0+dfsg-4+b1 [43.2 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 libboost-serialization1.62.0 amd64 1.62.0+dfsg-4+b1 [126 kB] Get:54 http://127.0.0.1:9999/debian unstable/main amd64 libboost-serialization1.62-dev amd64 1.62.0+dfsg-4+b1 [163 kB] Get:55 http://127.0.0.1:9999/debian unstable/main amd64 libboost-date-time1.62-dev amd64 1.62.0+dfsg-4+b1 [50.4 kB] Get:56 http://127.0.0.1:9999/debian unstable/main amd64 libboost-system1.62-dev amd64 1.62.0+dfsg-4+b1 [34.2 kB] Get:57 http://127.0.0.1:9999/debian unstable/main amd64 libboost-system-dev amd64 1.62.0.1 [3554 B] Get:58 http://127.0.0.1:9999/debian unstable/main amd64 libboost-thread1.62.0 amd64 1.62.0+dfsg-4+b1 [71.8 kB] Get:59 http://127.0.0.1:9999/debian unstable/main amd64 libboost-thread1.62-dev amd64 1.62.0+dfsg-4+b1 [71.6 kB] Get:60 http://127.0.0.1:9999/debian unstable/main amd64 libboost-thread-dev amd64 1.62.0.1 [3442 B] Get:61 http://127.0.0.1:9999/debian unstable/main amd64 seqan-dev all 1.4.2+dfsg-2 [1098 kB] Get:62 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 35.1 MB in 0s (80.7 MB/s) Selecting previously unselected package groff-base. (Reading database ... 10206 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_amd64.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_9.0.12+nmu1_amd64.deb ... Unpacking bsdmainutils (9.0.12+nmu1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../02-libpipeline1_1.4.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../03-man-db_2.7.6.1-2_amd64.deb ... Unpacking man-db (2.7.6.1-2) ... Selecting previously unselected package libpython2.7-minimal:amd64. Preparing to unpack .../04-libpython2.7-minimal_2.7.13-2_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.13-2) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../05-python2.7-minimal_2.7.13-2_amd64.deb ... Unpacking python2.7-minimal (2.7.13-2) ... 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Unpacking python (2.7.13-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../01-liblocale-gettext-perl_1.07-3+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.30-1_amd64.deb ... Unpacking libmagic-mgc (1:5.30-1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.30-1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.30-1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.30-1_amd64.deb ... Unpacking file (1:5.30-1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.19.8.1-2+b1_amd64.deb ... Unpacking gettext-base (0.19.8.1-2+b1) ... Selecting previously unselected package libicu57:amd64. Preparing to unpack .../06-libicu57_57.1-6_amd64.deb ... Unpacking libicu57:amd64 (57.1-6) ... 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Setting up libboost-serialization1.62-dev:amd64 (1.62.0+dfsg-4+b1) ... 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 libbam-dev (0.1.19-2) ... Setting up libsqlite3-0:amd64 (3.16.2-5) ... Setting up libboost-atomic1.62.0:amd64 (1.62.0+dfsg-4+b1) ... Setting up liblocale-gettext-perl (1.07-3+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 libpython2.7-stdlib:amd64 (2.7.13-2) ... Setting up autopoint (0.19.8.1-2) ... Setting up libboost-system1.62.0:amd64 (1.62.0+dfsg-4+b1) ... Setting up seqan-dev (1.4.2+dfsg-2) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-5) ... Setting up libfile-stripnondeterminism-perl (0.035-2) ... Setting up libboost-atomic1.62-dev:amd64 (1.62.0+dfsg-4+b1) ... Setting up libboost-date-time1.62-dev:amd64 (1.62.0+dfsg-4+b1) ... Setting up gettext (0.19.8.1-2+b1) ... Setting up libboost-thread1.62.0:amd64 (1.62.0+dfsg-4+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 libboost-system1.62-dev:amd64 (1.62.0+dfsg-4+b1) ... 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 libboost-chrono1.62.0:amd64 (1.62.0+dfsg-4+b1) ... Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up libboost-system-dev:amd64 (1.62.0.1) ... Setting up libboost-chrono1.62-dev:amd64 (1.62.0+dfsg-4+b1) ... Setting up libboost-thread1.62-dev:amd64 (1.62.0+dfsg-4+b1) ... Setting up libboost-thread-dev:amd64 (1.62.0.1) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.035-2) ... Setting up debhelper (10.6.2) ... Setting up sbuild-build-depends-tophat-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 libbam-dev_0.1.19-2 libblkid1_2.29.2-1 libboost-atomic1.62-dev_1.62.0+dfsg-4+b1 libboost-atomic1.62.0_1.62.0+dfsg-4+b1 libboost-chrono1.62-dev_1.62.0+dfsg-4+b1 libboost-chrono1.62.0_1.62.0+dfsg-4+b1 libboost-date-time1.62-dev_1.62.0+dfsg-4+b1 libboost-date-time1.62.0_1.62.0+dfsg-4+b1 libboost-serialization1.62-dev_1.62.0+dfsg-4+b1 libboost-serialization1.62.0_1.62.0+dfsg-4+b1 libboost-system-dev_1.62.0.1 libboost-system1.62-dev_1.62.0+dfsg-4+b1 libboost-system1.62.0_1.62.0+dfsg-4+b1 libboost-thread-dev_1.62.0.1 libboost-thread1.62-dev_1.62.0+dfsg-4+b1 libboost-thread1.62.0_1.62.0+dfsg-4+b1 libboost1.62-dev_1.62.0+dfsg-4+b1 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 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 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 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 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 libtimedate-perl_2.3000-2 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-core-dummy_0.invalid.0 sbuild-build-depends-tophat-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 seqan-dev_1.4.2+dfsg-2 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 Sat May 14 21:02:18 2016 UTC gpgv: using RSA key 578A0494D1C646D1 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./tophat_2.1.1+dfsg-2.dsc dpkg-source: info: extracting tophat in /<>/tophat-2.1.1+dfsg dpkg-source: info: unpacking tophat_2.1.1+dfsg.orig.tar.xz dpkg-source: info: unpacking tophat_2.1.1+dfsg-2.debian.tar.xz dpkg-source: info: applying hardening4samtools.patch dpkg-source: info: applying remove_3rd_party_code.patch dpkg-source: info: applying fix_includes_path.patch dpkg-source: info: applying fix-gcc6.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-3fafb28c-7d87-4f94-9ea8-c26c3b375b52 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package tophat dpkg-buildpackage: info: source version 2.1.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build tophat-2.1.1+dfsg dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with autoreconf dh_testdir dh_auto_clean dh_autoreconf_clean dh_clean debian/rules build-arch dh build-arch --with autoreconf dh_testdir -a dh_update_autotools_config -a dh_autoreconf -a sh: 1: git: not found sh: 1: git: not found sh: 1: git: not found sh: 1: git: not found sh: 1: git: not found configure.ac:20: installing './compile' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/tophat-2.1.1+dfsg' dh_auto_configure -- --with-boost-libdir=/usr/lib/x86_64-linux-gnu ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-boost-libdir=/usr/lib/x86_64-linux-gnu configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for ar... ar checking the archiver (ar) interface... ar checking for gawk... (cached) mawk checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) none checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking whether make sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking for a Python interpreter with version >= 2.4... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/dist-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages checking for boostlib >= 1.38.0... yes checking whether the compiler implements namespaces... yes checking whether the Boost::Thread library is available... yes checking for main in -lboost_thread... yes checking whether Boost::Thread needs Boost::System library... yes checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for ANSI C header files... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... no checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for ptrdiff_t... yes checking for an ANSI C-conforming const... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for gzread in -lz... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for memset... yes checking for strdup... yes checking for strrchr... yes checking for strtol... yes checking for strsep... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to create a pax tar archive... gnutar checking dependency style of gcc... (cached) none checking dependency style of g++... (cached) none checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode -- tophat 2.1.1 Configuration Results -- C++ compiler: g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include Linker flags: -L./samtools-0.1.18 -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now BOOST libraries: -lboost_thread -lboost_system GCC version: clang version 4.0.1-1 (tags/RELEASE_401/final) Host System type: x86_64-pc-linux-gnu Install prefix: /usr Install eprefix: ${prefix} See config.h for further configuration information. Email bug reports to . make[1]: Leaving directory '/<>/tophat-2.1.1+dfsg' dh_auto_build -a make -j1 make[1]: Entering directory '/<>/tophat-2.1.1+dfsg' make all-recursive make[2]: Entering directory '/<>/tophat-2.1.1+dfsg' Making all in src make[3]: Entering directory '/<>/tophat-2.1.1+dfsg/src' Makefile:1765: warning: overriding recipe for target 'libbam.a' Makefile:1292: warning: ignoring old recipe for target 'libbam.a' cd ./samtools-0.1.18 && make samtools_0.1.18 && cp libbam.a samtools_0.1.18 .. make[4]: Entering directory '/<>/tophat-2.1.1+dfsg/src/samtools-0.1.18' make[5]: Entering directory '/<>/tophat-2.1.1+dfsg/src/samtools-0.1.18' gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bgzf.c -o bgzf.o bgzf.c:275:17: warning: implicit conversion from 'const int' to 'bgzf_byte_t' (aka 'signed char') changes value from 139 to -117 [-Wconstant-conversion] buffer[1] = GZIP_ID2; ~ ^~~~~~~~ bgzf.c:283:17: warning: implicit conversion from 'const int' to 'bgzf_byte_t' (aka 'signed char') changes value from 255 to -1 [-Wconstant-conversion] buffer[9] = OS_UNKNOWN; ~ ^~~~~~~~~~ bgzf.c:44:1: warning: unused function 'kh_clear_cache' [-Wunused-function] KHASH_MAP_INIT_INT64(cache, cache_t) ^ ./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :113:1: note: expanded from here kh_clear_cache ^ 3 warnings generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kstring.c -o kstring.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_aux.c -o bam_aux.o bam_aux.c:5:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :90:1: note: expanded from here kh_clear_s ^ bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function] ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :104:1: note: expanded from here kh_del_s ^ bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function] KHASH_MAP_INIT_STR(r2l, str_p) ^ ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :111:1: note: expanded from here kh_init_r2l ^ bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function] ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :116:1: note: expanded from here kh_destroy_r2l ^ bam_aux.c:6:1: warning: unused function 'kh_clear_r2l' [-Wunused-function] ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :119:1: note: expanded from here kh_clear_r2l ^ bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function] ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :122:1: note: expanded from here kh_get_r2l ^ bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function] ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :128:1: note: expanded from here kh_put_r2l ^ bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function] ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :133:1: note: expanded from here kh_del_r2l ^ 8 warnings generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam.c -o bam.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_import.c -o bam_import.o bam_import.c:18:1: warning: unused function 'kh_clear_ref' [-Wunused-function] KHASH_MAP_INIT_STR(ref, uint64_t) ^ ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :100:1: note: expanded from here kh_clear_ref ^ bam_import.c:18:1: warning: unused function 'kh_get_ref' [-Wunused-function] ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :103:1: note: expanded from here kh_get_ref ^ bam_import.c:18:1: warning: unused function 'kh_del_ref' [-Wunused-function] ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :114:1: note: expanded from here kh_del_ref ^ 3 warnings generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam.c -o sam.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_index.c -o bam_index.o bam_index.c:64:1: warning: unused function 'kh_clear_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, bam_binlist_t) ^ ./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :105:1: note: expanded from here kh_clear_i ^ bam_index.c:64:1: warning: unused function 'kh_del_i' [-Wunused-function] ./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :119:1: note: expanded from here kh_del_i ^ 2 warnings generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_pileup.c -o bam_pileup.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_md.c -o bam_md.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. razf.c -o razf.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. faidx.c -o faidx.o faidx.c:14:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, faidx1_t) ^ ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :74:1: note: expanded from here kh_clear_s ^ faidx.c:14:1: warning: unused function 'kh_del_s' [-Wunused-function] ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :88:1: note: expanded from here kh_del_s ^ 2 warnings generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bedidx.c -o bedidx.o bedidx.c:24:1: warning: unused function 'kh_clear_reg' [-Wunused-function] KHASH_MAP_INIT_STR(reg, bed_reglist_t) ^ ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :100:1: note: expanded from here kh_clear_reg ^ bedidx.c:24:1: warning: unused function 'kh_del_reg' [-Wunused-function] ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :114:1: note: expanded from here kh_del_reg ^ 2 warnings generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. knetfile.c -o knetfile.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_sort.c -o bam_sort.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam_header.c -o sam_header.o sam_header.c:9:1: warning: unused function 'kh_clear_str' [-Wunused-function] KHASH_MAP_INIT_STR(str, const char *) ^ ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :73:1: note: expanded from here kh_clear_str ^ sam_header.c:9:1: warning: unused function 'kh_del_str' [-Wunused-function] ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :87:1: note: expanded from here kh_del_str ^ 2 warnings generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_reheader.c -o bam_reheader.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kprobaln.c -o kprobaln.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_cat.c -o bam_cat.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') make[5]: Leaving directory '/<>/tophat-2.1.1+dfsg/src/samtools-0.1.18' make[5]: Entering directory '/<>/tophat-2.1.1+dfsg/src/samtools-0.1.18/bcftools' gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcf.c -o bcf.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. vcf.c -o vcf.o vcf.c:238:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] endblock: i = i; ~ ^ ~ vcf.c:8:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 4096) ^ ../kseq.h:142:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ ../kseq.h:66:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 2 warnings generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcfutils.c -o bcfutils.o bcfutils.c:6:1: warning: unused function 'kh_clear_str2id' [-Wunused-function] KHASH_MAP_INIT_STR(str2id, int) ^ ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ../khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :154:1: note: expanded from here kh_clear_str2id ^ bcfutils.c:6:1: warning: unused function 'kh_del_str2id' [-Wunused-function] ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ../khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :168:1: note: expanded from here kh_del_str2id ^ 2 warnings generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. prob1.c -o prob1.o prob1.c:10:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 16384) ^ ../kseq.h:142:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ ../kseq.h:66:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. em.c -o em.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. kfunc.c -o kfunc.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. kmin.c -o kmin.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. index.c -o index.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. fet.c -o fet.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. mut.c -o mut.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcf2qcall.c -o bcf2qcall.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o ar: `u' modifier ignored since `D' is the default (see `U') make[5]: Leaving directory '/<>/tophat-2.1.1+dfsg/src/samtools-0.1.18/bcftools' gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_tview.c -o bam_tview.o bam_tview.c:434:2: warning: "No curses library is available; tview is disabled." [-W#warnings] #warning "No curses library is available; tview is disabled." ^ 1 warning generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_plcmd.c -o bam_plcmd.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam_view.c -o sam_view.o sam_view.c:11:1: warning: unused function 'kh_clear_rg' [-Wunused-function] KHASH_SET_INIT_STR(rg) ^ ./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :163:1: note: expanded from here kh_clear_rg ^ sam_view.c:11:1: warning: unused function 'kh_del_rg' [-Wunused-function] ./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :177:1: note: expanded from here kh_del_rg ^ 2 warnings generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_rmdup.c -o bam_rmdup.o bam_rmdup.c:12:1: warning: unused function 'kh_get_pos' [-Wunused-function] KHASH_MAP_INIT_INT64(pos, bam1_p) ^ ./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :130:1: note: expanded from here kh_get_pos ^ bam_rmdup.c:12:1: warning: unused function 'kh_del_pos' [-Wunused-function] ./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :141:1: note: expanded from here kh_del_pos ^ bam_rmdup.c:20:1: warning: unused function 'kh_clear_lib' [-Wunused-function] KHASH_MAP_INIT_STR(lib, lib_aux_t) ^ ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :158:1: note: expanded from here kh_clear_lib ^ bam_rmdup.c:20:1: warning: unused function 'kh_del_lib' [-Wunused-function] ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :172:1: note: expanded from here kh_del_lib ^ 4 warnings generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_rmdupse.c -o bam_rmdupse.o bam_rmdupse.c:18:1: warning: unused function 'kh_clear_best' [-Wunused-function] KHASH_MAP_INIT_INT(best, elem_p) ^ ./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :208:1: note: expanded from here kh_clear_best ^ bam_rmdupse.c:18:1: warning: unused function 'kh_get_best' [-Wunused-function] ./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :211:1: note: expanded from here kh_get_best ^ bam_rmdupse.c:25:1: warning: unused function 'kh_clear_lib' [-Wunused-function] KHASH_MAP_INIT_STR(lib, lib_aux_t) ^ ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :239:1: note: expanded from here kh_clear_lib ^ bam_rmdupse.c:25:1: warning: unused function 'kh_del_lib' [-Wunused-function] ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :253:1: note: expanded from here kh_del_lib ^ 4 warnings generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_mate.c -o bam_mate.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_stat.c -o bam_stat.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_color.c -o bam_color.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bamtk.c -o bamtk.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kaln.c -o kaln.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2bcf.c -o bam2bcf.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2bcf_indel.c -o bam2bcf_indel.o bam2bcf_indel.c:32:52: warning: for loop has empty body [-Wempty-body] for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p; ^ bam2bcf_indel.c:32:52: note: put the semicolon on a separate line to silence this warning bam2bcf_indel.c:33:52: warning: for loop has empty body [-Wempty-body] for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q; ^ bam2bcf_indel.c:33:52: note: put the semicolon on a separate line to silence this warning bam2bcf_indel.c:9:1: warning: unused function 'kh_clear_rg' [-Wunused-function] KHASH_SET_INIT_STR(rg) ^ ./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :96:1: note: expanded from here kh_clear_rg ^ bam2bcf_indel.c:9:1: warning: unused function 'kh_del_rg' [-Wunused-function] ./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :110:1: note: expanded from here kh_del_rg ^ 4 warnings generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. errmod.c -o errmod.o errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare] if (m > m) return -1; ^ 1 warning generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sample.c -o sample.o sample.c:5:1: warning: unused function 'kh_clear_sm' [-Wunused-function] KHASH_MAP_INIT_STR(sm, int) ^ ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :45:1: note: expanded from here kh_clear_sm ^ sample.c:5:1: warning: unused function 'kh_del_sm' [-Wunused-function] ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :59:1: note: expanded from here kh_del_sm ^ 2 warnings generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. cut_target.c -o cut_target.o gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. phase.c -o phase.o phase.c:45:1: warning: unused function 'kh_clear_set64' [-Wunused-function] KHASH_SET_INIT_INT64(set64) ^ ./khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64' KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :163:1: note: expanded from here kh_clear_set64 ^ phase.c:45:1: warning: unused function 'kh_del_set64' [-Wunused-function] ./khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64' KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :177:1: note: expanded from here kh_del_set64 ^ phase.c:46:1: warning: unused function 'kh_clear_64' [-Wunused-function] KHASH_MAP_INIT_INT64(64, frag_t) ^ ./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :192:1: note: expanded from here kh_clear_64 ^ 3 warnings generated. gcc -c -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2depth.c -o bam2depth.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 -fdebug-prefix-map=/<>/tophat-2.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -o samtools_0.1.18 bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lm -lz -L./samtools-0.1.18 -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now #-lcurses libbam.a(bam_sort.o): In function `ks_combsort_heap': ./src/samtools-0.1.18/bam_sort.c:53: undefined reference to `__ks_insertsort_heap' libbam.a(bam_sort.o): In function `ks_introsort_heap': ./src/samtools-0.1.18/bam_sort.c:53: undefined reference to `__ks_insertsort_heap' clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:44: recipe for target 'samtools_0.1.18' failed make[4]: *** [samtools_0.1.18] Error 1 make[4]: Leaving directory '/<>/tophat-2.1.1+dfsg/src/samtools-0.1.18' Makefile:1765: recipe for target 'libbam.a' failed make[3]: *** [libbam.a] Error 2 make[3]: Leaving directory '/<>/tophat-2.1.1+dfsg/src' Makefile:387: recipe for target 'all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory '/<>/tophat-2.1.1+dfsg' Makefile:328: recipe for target 'all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory '/<>/tophat-2.1.1+dfsg' dh_auto_build: make -j1 returned exit code 2 debian/rules:13: 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 2017-07-06T19:34:20Z 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: 7928 Build-Time: 23 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 11 Job: tophat_2.1.1+dfsg-2 Machine Architecture: amd64 Package: tophat Package-Time: 50 Source-Version: 2.1.1+dfsg-2 Space: 7928 Status: attempted Version: 2.1.1+dfsg-2 -------------------------------------------------------------------------------- Finished at 2017-07-06T19:34:20Z Build needed 00:00:50, 7928k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 50.708528211s DC-Time-Estimation: 50.708528211 versus expected 477 (r/m: 8.406701729050111 ; m: 50.708528211)