DC-Build-Header: libvcflib 1.0.0~rc1+dfsg1-5 / 2017-07-06 15:48:15 +0000 DC-Task: type:rebuild-binarch-only source:libvcflib version:1.0.0~rc1+dfsg1-5 chroot:unstable esttime: logfile:/tmp/libvcflib_1.0.0~rc1+dfsg1-5_unstable_clang3.9.log modes:clang:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang libvcflib_1.0.0~rc1+dfsg1-5' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-45-63.eu-central-1.compute.internal +==============================================================================+ | libvcflib 1.0.0~rc1+dfsg1-5 (amd64) Thu, 06 Jul 2017 15:48:15 +0000 | +==============================================================================+ Package: libvcflib Version: 1.0.0~rc1+dfsg1-5 Source Version: 1.0.0~rc1+dfsg1-5 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-a736fe99-dfaf-4f30-ba07-337e2fbf273d' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang ---------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=3.9 + echo 'Install of clang-3.9' Install of clang-3.9 + apt-get update Get:1 http://127.0.0.1:9999/debian unstable InRelease [255 kB] Get:2 http://127.0.0.1:9999/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:9999/debian unstable/main Translation-en.diff/Index [27.9 kB] Get:5 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-02-0216.39.pdiff [15.0 kB] Get:6 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-02-0817.00.pdiff [7416 B] Get:7 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-02-1415.16.pdiff [17.0 kB] Get:8 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-02-2015.53.pdiff [15.2 kB] Get:9 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-03-0215.43.pdiff [50.2 kB] Get:10 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-03-0815.58.pdiff [5500 B] Get:11 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Building dependency tree... Reading state information... The following additional packages will be installed: cpp-6 g++-6 gcc-6 gcc-6-base gcc-7-base libasan3 libatomic1 libbsd0 libcc1-0 libcilkrts5 libclang-common-3.9-dev libclang1-3.9 libedit2 libffi6 libgcc-6-dev libgcc1 libgomp1 libitm1 libjsoncpp1 libllvm3.9 liblsan0 libmpx2 libncurses5 libobjc-6-dev libobjc4 libquadmath0 libstdc++-6-dev libstdc++6 libtsan0 libubsan0 Suggested packages: gnustep gnustep-devel clang-3.9-doc gcc-6-locales g++-6-multilib gcc-6-doc libstdc++6-6-dbg gcc-6-multilib libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg libasan3-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg libmpx2-dbg libquadmath0-dbg libstdc++-6-doc Recommended packages: llvm-3.9-dev python libgpm2 The following NEW packages will be installed: clang-3.9 libbsd0 libclang-common-3.9-dev libclang1-3.9 libedit2 libffi6 libjsoncpp1 libllvm3.9 libncurses5 libobjc-6-dev libobjc4 The following packages will be upgraded: cpp-6 g++-6 gcc-6 gcc-6-base gcc-7-base libasan3 libatomic1 libcc1-0 libcilkrts5 libgcc-6-dev libgcc1 libgomp1 libitm1 liblsan0 libmpx2 libquadmath0 libstdc++-6-dev libstdc++6 libtsan0 libubsan0 20 upgraded, 11 newly installed, 0 to remove and 13 not upgraded. Need to get 83.9 MB of archives. After this operation, 251 MB of additional disk space will be used. 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Preparing to unpack .../16-libclang-common-3.9-dev_1%3a3.9.1-10_amd64.deb ... Unpacking libclang-common-3.9-dev (1:3.9.1-10) ... Selecting previously unselected package clang-3.9. Preparing to unpack .../17-clang-3.9_1%3a3.9.1-10_amd64.deb ... Unpacking clang-3.9 (1:3.9.1-10) ... Setting up libquadmath0:amd64 (7.1.0-9) ... Setting up libncurses5:amd64 (6.0+20161126-1) ... Setting up libgomp1:amd64 (7.1.0-9) ... Setting up libatomic1:amd64 (7.1.0-9) ... Setting up libcc1-0:amd64 (7.1.0-9) ... Setting up libobjc4:amd64 (7.1.0-9) ... Setting up libcilkrts5:amd64 (7.1.0-9) ... Setting up libubsan0:amd64 (7.1.0-9) ... Setting up libtsan0:amd64 (7.1.0-9) ... Setting up gcc-6-base:amd64 (6.4.0-1) ... Setting up libbsd0:amd64 (0.8.5-1) ... Setting up liblsan0:amd64 (7.1.0-9) ... Setting up libmpx2:amd64 (7.1.0-9) ... Processing triggers for libc-bin (2.24-12) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up cpp-6 (6.4.0-1) ... Setting up libitm1:amd64 (7.1.0-9) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libedit2:amd64 (3.1-20170329-1) ... Setting up libasan3:amd64 (6.4.0-1) ... Setting up libgcc-6-dev:amd64 (6.4.0-1) ... Setting up libstdc++-6-dev:amd64 (6.4.0-1) ... Setting up libllvm3.9:amd64 (1:3.9.1-10) ... Setting up libclang-common-3.9-dev (1:3.9.1-10) ... Setting up gcc-6 (6.4.0-1) ... Setting up g++-6 (6.4.0-1) ... Setting up libobjc-6-dev:amd64 (6.4.0-1) ... Setting up libclang1-3.9:amd64 (1:3.9.1-10) ... Setting up clang-3.9 (1:3.9.1-10) ... 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++-3.9 g++-4.6 + ln -s clang-3.9 gcc-4.6 + ln -s clang-3.9 cpp-4.6 + ln -s clang-3.9 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++-3.9 g++-4.7 + ln -s clang-3.9 gcc-4.7 + ln -s clang-3.9 cpp-4.7 + ln -s clang-3.9 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++-3.9 g++-4.8 + ln -s clang-3.9 gcc-4.8 + ln -s clang-3.9 cpp-4.8 + ln -s clang-3.9 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++-3.9 g++-4.9 + ln -s clang-3.9 gcc-4.9 + ln -s clang-3.9 cpp-4.9 + ln -s clang-3.9 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++-3.9 g++-5 + ln -s clang-3.9 gcc-5 + ln -s clang-3.9 cpp-5 + ln -s clang-3.9 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++-3.9 g++-6 + ln -s clang-3.9 gcc-6 + ln -s clang-3.9 cpp-6 + ln -s clang-3.9 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++-3.9 g++-7 + ln -s clang-3.9 gcc-7 + ln -s clang-3.9 cpp-7 + ln -s clang-3.9 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/libvcflib-VhWkB5 + 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/clang'. 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... The following NEW packages will be installed: libgnutls30 libhogweed4 libidn2-0 libnettle6 libp11-kit0 libtasn1-6 libunistring2 The following packages will be upgraded: apt cpp debconf g++ gcc libapt-pkg5.0 libdebconfclient0 libperl5.24 libsystemd0 libudev1 perl perl-base perl-modules-5.24 13 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. Need to get 12.5 MB of archives. After this operation, 6330 kB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libperl5.24 amd64 5.24.1-6 [3525 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 perl amd64 5.24.1-6 [218 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 perl-base amd64 5.24.1-6 [1344 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 perl-modules-5.24 all 5.24.1-6 [2723 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libapt-pkg5.0 amd64 1.5~beta1 [922 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libnettle6 amd64 3.3-1+b1 [191 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libhogweed4 amd64 3.3-1+b1 [136 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libunistring2 amd64 0.9.7-2 [377 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 libidn2-0 amd64 0.16-1+b1 [56.6 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 libp11-kit0 amd64 0.23.7-2 [193 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 libtasn1-6 amd64 4.12-2 [51.0 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libgnutls30 amd64 3.5.13-2 [914 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 apt amd64 1.5~beta1 [1237 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 debconf all 1.5.62 [160 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 libsystemd0 amd64 233-10 [281 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 libudev1 amd64 233-10 [126 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libdebconfclient0 amd64 0.229 [47.9 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 cpp amd64 4:6.3.0-4d1 [18.8 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 gcc amd64 4:6.3.0-4d1 [5252 B] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 g++ amd64 4:6.3.0-4d1 [1548 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.5 MB in 0s (87.9 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 10176 files and directories currently installed.) Preparing to unpack .../cpp_4%3a6.3.0-4d1_amd64.deb ... Unpacking cpp (4:6.3.0-4d1) over (4:6.3.0-4) ... Preparing to unpack .../gcc_4%3a6.3.0-4d1_amd64.deb ... Removing old gcc doc directory. Unpacking gcc (4:6.3.0-4d1) over (4:6.3.0-4) ... Preparing to unpack .../g++_4%3a6.3.0-4d1_amd64.deb ... Unpacking g++ (4:6.3.0-4d1) over (4:6.3.0-4) ... Setting up cpp (4:6.3.0-4d1) ... Setting up perl-modules-5.24 (5.24.1-6) ... Setting up libperl5.24:amd64 (5.24.1-6) ... Setting up gcc (4:6.3.0-4d1) ... Setting up perl (5.24.1-6) ... Processing triggers for libc-bin (2.24-12) ... Setting up g++ (4:6.3.0-4d1) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'libvcflib' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/libvcflib.git Please use: git clone https://anonscm.debian.org/git/debian-med/libvcflib.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 6609 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main libvcflib 1.0.0~rc1+dfsg1-5 (dsc) [2318 B] Get:2 http://127.0.0.1:9999/debian unstable/main libvcflib 1.0.0~rc1+dfsg1-5 (tar) [6596 kB] Get:3 http://127.0.0.1:9999/debian unstable/main libvcflib 1.0.0~rc1+dfsg1-5 (diff) [10.8 kB] Fetched 6609 kB in 0s (38.8 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/libvcflib-VhWkB5/libvcflib-1.0.0~rc1+dfsg1' with '<>' I: NOTICE: Log filtering will replace 'build/libvcflib-VhWkB5' 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-nT2L7K/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-nT2L7K/apt_archive ./ InRelease Get:2 copy:/<>/resolver-nT2L7K/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-nT2L7K/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-nT2L7K/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-nT2L7K/apt_archive ./ Packages [430 B] Fetched 1736 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 784 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-nT2L7K/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [784 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 784 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10178 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 any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 10), dh-exec, python-markdown, libtabixpp-dev, libdisorder-dev, libsmithwaterman-dev (>= 0.0+20160702-2), libssw-dev, libfastahack-dev, pkg-config, libipc-run3-perl Filtered Build-Depends: debhelper (>= 10), dh-exec, python-markdown, libtabixpp-dev, libdisorder-dev, libsmithwaterman-dev (>= 0.0+20160702-2), libssw-dev, libfastahack-dev, pkg-config, libipc-run3-perl dpkg-deb: building package 'sbuild-build-depends-libvcflib-dummy' in '/<>/resolver-nT2L7K/apt_archive/sbuild-build-depends-libvcflib-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-libvcflib-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-nT2L7K/apt_archive ./ InRelease Get:2 copy:/<>/resolver-nT2L7K/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-nT2L7K/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-nT2L7K/apt_archive ./ Sources [586 B] Get:5 copy:/<>/resolver-nT2L7K/apt_archive ./ Packages [664 B] Fetched 2213 B in 0s (0 B/s) Reading package lists... Reading package lists... Install libvcflib 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-exec dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3 libcurl3-gnutls libdisorder-dev libdisorder0 libexpat1 libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts2 libicu57 libipc-run3-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsmithwaterman-dev libsmithwaterman0 libsqlite3-0 libssh2-1 libssl1.1 libssw-dev libssw0 libtabixpp-dev libtabixpp0 libtimedate-perl libtool libxml2 m4 man-db mime-support pkg-config po-debconf python python-markdown 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 krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk python-markdown-doc python2.7-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx-cur ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev xml-core libmail-sendmail-perl python-pygments python-yaml The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-exec dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3 libcurl3-gnutls libdisorder-dev libdisorder0 libexpat1 libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts2 libicu57 libipc-run3-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsmithwaterman-dev libsmithwaterman0 libsqlite3-0 libssh2-1 libssl1.1 libssw-dev libssw0 libtabixpp-dev libtabixpp0 libtimedate-perl libtool libxml2 m4 man-db mime-support pkg-config po-debconf python python-markdown python-minimal python2.7 python2.7-minimal readline-common sbuild-build-depends-libvcflib-dummy zlib1g-dev 0 upgraded, 73 newly installed, 0 to remove and 0 not upgraded. Need to get 28.7 MB of archives. After this operation, 96.6 MB of additional disk space will be used. Get:1 copy:/<>/resolver-nT2L7K/apt_archive ./ sbuild-build-depends-libvcflib-dummy 0.invalid.0 [882 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 libmagic-mgc amd64 1:5.30-1 [222 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.30-1 [111 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.30-1 [63.9 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-2+b1 [122 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5support0 amd64 1.15-1 [61.7 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 libk5crypto3 amd64 1.15-1 [119 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5-3 amd64 1.15-1 [311 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.15-1 [154 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3 [68.2 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3 [105 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 libldap-common all 2.4.44+dfsg-7 [85.2 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-7 [219 kB] Get:32 http://127.0.0.1:9999/debian unstable/main 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libfile-stripnondeterminism-perl all 0.035-2 [17.0 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.035-2 [10.7 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.52.3-1 [2742 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.12-1 [144 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-2+b1 [1301 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.20 [247 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 10.6.2 [968 kB] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 dh-exec amd64 0.23+b1 [26.7 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 libnghttp2-14 amd64 1.24.0-1 [81.6 kB] Get:54 http://127.0.0.1:9999/debian unstable/main amd64 libpsl5 amd64 0.17.0-4+b1 [43.0 kB] Get:55 http://127.0.0.1:9999/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:56 http://127.0.0.1:9999/debian unstable/main amd64 libssh2-1 amd64 1.8.0-1 [138 kB] Get:57 http://127.0.0.1:9999/debian unstable/main amd64 libcurl3-gnutls amd64 7.52.1-5 [289 kB] Get:58 http://127.0.0.1:9999/debian unstable/main amd64 libdisorder0 amd64 0.0.2-1 [3962 B] Get:59 http://127.0.0.1:9999/debian unstable/main amd64 libdisorder-dev amd64 0.0.2-1 [3916 B] Get:60 http://127.0.0.1:9999/debian unstable/main amd64 libfastahack0 amd64 0.0+20160702-1+b1 [22.1 kB] Get:61 http://127.0.0.1:9999/debian unstable/main amd64 libfastahack-dev amd64 0.0+20160702-1+b1 [22.9 kB] Get:62 http://127.0.0.1:9999/debian unstable/main amd64 libhts2 amd64 1.4.1-2 [294 kB] Get:63 http://127.0.0.1:9999/debian unstable/main amd64 libhts-dev amd64 1.4.1-2 [398 kB] Get:64 http://127.0.0.1:9999/debian unstable/main amd64 libipc-run3-perl all 0.048-1 [37.8 kB] Get:65 http://127.0.0.1:9999/debian unstable/main amd64 libsmithwaterman0 amd64 0.0+20160702-3 [33.0 kB] Get:66 http://127.0.0.1:9999/debian unstable/main amd64 libsmithwaterman-dev amd64 0.0+20160702-3 [36.8 kB] Get:67 http://127.0.0.1:9999/debian unstable/main amd64 libssw0 amd64 1.1-1+b1 [16.5 kB] Get:68 http://127.0.0.1:9999/debian unstable/main amd64 libssw-dev amd64 1.1-1+b1 [19.4 kB] Get:69 http://127.0.0.1:9999/debian unstable/main amd64 libtabixpp0 amd64 1.0.0-3 [7624 B] Get:70 http://127.0.0.1:9999/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-5 [205 kB] Get:71 http://127.0.0.1:9999/debian unstable/main amd64 libtabixpp-dev amd64 1.0.0-3 [6968 B] Get:72 http://127.0.0.1:9999/debian unstable/main amd64 pkg-config amd64 0.29-4+b1 [63.3 kB] Get:73 http://127.0.0.1:9999/debian unstable/main amd64 python-markdown all 2.6.8-1 [58.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.7 MB in 0s (54.2 MB/s) Selecting previously unselected package groff-base. 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Selecting previously unselected package pkg-config. Preparing to unpack .../54-pkg-config_0.29-4+b1_amd64.deb ... Unpacking pkg-config (0.29-4+b1) ... Selecting previously unselected package python-markdown. Preparing to unpack .../55-python-markdown_2.6.8-1_all.deb ... Unpacking python-markdown (2.6.8-1) ... Selecting previously unselected package sbuild-build-depends-libvcflib-dummy. Preparing to unpack .../56-sbuild-build-depends-libvcflib-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-libvcflib-dummy (0.invalid.0) ... Setting up readline-common (7.0-3) ... Setting up libexpat1:amd64 (2.2.1-3) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up libdisorder0:amd64 (0.0.2-1) ... Setting up libnghttp2-14:amd64 (1.24.0-1) ... Setting up libfastahack0 (0.0+20160702-1+b1) ... Setting up mime-support (3.60) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:amd64 (2.11-1) ... Setting up libldap-common (2.4.44+dfsg-7) ... Setting up libssw0:amd64 (1.1-1+b1) ... Setting up libreadline7:amd64 (7.0-3) ... Setting up libpsl5:amd64 (0.17.0-4+b1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:amd64 (2.52.3-1) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3) ... Setting up libssw-dev:amd64 (1.1-1+b1) ... Setting up libdisorder-dev:amd64 (0.0.2-1) ... Setting up gettext-base (0.19.8.1-2+b1) ... Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:amd64 (57.1-6) ... 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) ... Setting up libfastahack-dev (0.0+20160702-1+b1) ... Setting up pkg-config (0.29-4+b1) ... Setting up libssh2-1:amd64 (1.8.0-1) ... Processing triggers for libc-bin (2.24-12) ... Setting up autotools-dev (20161112.1) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-7) ... Setting up libssl1.1:amd64 (1.1.0f-3) ... Setting up libsqlite3-0:amd64 (3.16.2-5) ... Setting up libipc-run3-perl (0.048-1) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... 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 libsmithwaterman0 (0.0+20160702-3) ... 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 libkrb5support0:amd64 (1.15-1) ... Setting up libsmithwaterman-dev (0.0+20160702-3) ... 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 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 python-markdown (2.6.8-1) ... Setting up libtool (2.4.6-2) ... Setting up libk5crypto3:amd64 (1.15-1) ... Setting up po-debconf (1.0.20) ... Setting up libkrb5-3:amd64 (1.15-1) ... Setting up libgssapi-krb5-2:amd64 (1.15-1) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5) ... Setting up libhts2:amd64 (1.4.1-2) ... Setting up libtabixpp0:amd64 (1.0.0-3) ... Setting up libhts-dev:amd64 (1.4.1-2) ... Setting up libtabixpp-dev:amd64 (1.0.0-3) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.035-2) ... Setting up debhelper (10.6.2) ... Setting up dh-exec (0.23+b1) ... Setting up sbuild-build-depends-libvcflib-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-3.9_1:3.9.1-10 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-exec_0.23+b1 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 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-3.9-dev_1:3.9.1-10 libclang1-3.9_1:3.9.1-10 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcurl3-gnutls_7.52.1-5 libdb5.3_5.3.28-12+b1 libdebconfclient0_0.229 libdisorder-dev_0.0.2-1 libdisorder0_0.0.2-1 libdpkg-perl_1.18.24 libeatmydata1_105-5 libedit2_3.1-20170329-1 libexpat1_2.2.1-3 libfakeroot_1.21-3.1 libfastahack-dev_0.0+20160702-1+b1 libfastahack0_0.0+20160702-1+b1 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 libgssapi-krb5-2_1.15-1 libhogweed4_3.3-1+b1 libhts-dev_1.4.1-2 libhts2_1.4.1-2 libicu57_57.1-6 libidn2-0_0.16-1+b1 libipc-run3-perl_0.048-1 libisl15_0.18-1 libitm1_7.1.0-9 libjsoncpp1_1.7.4-3 libk5crypto3_1.15-1 libkeyutils1_1.5.9-9 libkrb5-3_1.15-1 libkrb5support0_1.15-1 libldap-2.4-2_2.4.44+dfsg-7 libldap-common_2.4.44+dfsg-7 libllvm3.9_1:3.9.1-10 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 libnghttp2-14_1.24.0-1 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 libpsl5_0.17.0-4+b1 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 librtmp1_2.4+20151223.gitfa8646d.1-1+b1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-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 libsmithwaterman-dev_0.0+20160702-3 libsmithwaterman0_0.0+20160702-3 libsqlite3-0_3.16.2-5 libss2_1.43.4-2 libssh2-1_1.8.0-1 libssl1.1_1.1.0f-3 libssw-dev_1.1-1+b1 libssw0_1.1-1+b1 libstdc++-6-dev_6.4.0-1 libstdc++6_7.1.0-9 libsystemd0_233-10 libtabixpp-dev_1.0.0-3 libtabixpp0_1.0.0-3 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 pkg-config_0.29-4+b1 po-debconf_1.0.20 python_2.7.13-2 python-markdown_2.6.8-1 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-libvcflib-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 Sat Jun 17 21:49:31 2017 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libvcflib_1.0.0~rc1+dfsg1-5.dsc dpkg-source: info: extracting libvcflib in /<>/libvcflib-1.0.0~rc1+dfsg1 dpkg-source: info: unpacking libvcflib_1.0.0~rc1+dfsg1.orig.tar.xz dpkg-source: info: unpacking libvcflib_1.0.0~rc1+dfsg1-5.debian.tar.xz dpkg-source: info: applying use_debian_packaged_tabixpp.patch dpkg-source: info: applying use_debian_packaged_smithwaterman.patch dpkg-source: info: applying multichoose.h.patch dpkg-source: info: applying filevercmp.h.patch dpkg-source: info: applying use_debian_packaged_fastahack.patch dpkg-source: info: applying intervaltree.patch dpkg-source: info: applying shared_lib.patch dpkg-source: info: applying keep_R_files.patch dpkg-source: info: applying use_debian_packaged_libssw.patch dpkg-source: info: applying pkg-config.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-a736fe99-dfaf-4f30-ba07-337e2fbf273d SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package libvcflib dpkg-buildpackage: info: source version 1.0.0~rc1+dfsg1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build libvcflib-1.0.0~rc1+dfsg1 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean make -j16 clean make[1]: Entering directory '/<>/libvcflib-1.0.0~rc1+dfsg1' make[1]: git: Command not found rm -f binaries/vcfecho binaries/dumpContigsFromHeader binaries/bFst binaries/hapLrt binaries/popStats binaries/wcFst binaries/iHS binaries/segmentFst binaries/segmentIhs binaries/genotypeSummary binaries/sequenceDiversity binaries/pFst binaries/smoother binaries/LD binaries/plotHaps binaries/abba-baba binaries/permuteGPAT++ binaries/permuteSmooth binaries/normalize-iHS binaries/meltEHH binaries/vcfaltcount binaries/vcfhetcount binaries/vcfhethomratio binaries/vcffilter binaries/vcf2tsv binaries/vcfgenotypes binaries/vcfannotategenotypes binaries/vcfcommonsamples binaries/vcfremovesamples binaries/vcfkeepsamples binaries/vcfsamplenames binaries/vcfgenotypecompare binaries/vcffixup binaries/vcfclassify binaries/vcfsamplediff binaries/vcfremoveaberrantgenotypes binaries/vcfrandom binaries/vcfparsealts binaries/vcfstats binaries/vcfflatten binaries/vcfprimers binaries/vcfnumalt binaries/vcfcleancomplex binaries/vcfintersect binaries/vcfannotate binaries/vcfallelicprimitives binaries/vcfoverlay binaries/vcfaddinfo binaries/vcfkeepinfo binaries/vcfkeepgeno binaries/vcfafpath binaries/vcfcountalleles binaries/vcflength binaries/vcfdistance binaries/vcfrandomsample binaries/vcfentropy binaries/vcfglxgt binaries/vcfroc binaries/vcfcheck binaries/vcfstreamsort binaries/vcfuniq binaries/vcfuniqalleles binaries/vcfremap binaries/vcf2fasta binaries/vcfsitesummarize binaries/vcfbreakmulti binaries/vcfcreatemulti binaries/vcfevenregions binaries/vcfcat binaries/vcfgenosummarize binaries/vcfgenosamplenames binaries/vcfgeno2haplo binaries/vcfleftalign binaries/vcfcombine binaries/vcfgeno2alleles binaries/vcfindex binaries/vcf2dag binaries/vcfsample2info binaries/vcfqual2info binaries/vcfinfo2qual binaries/vcfglbound binaries/vcfinfosummarize src/Variant.o src/rnglib.o src/var.o src/pdflib.o src/cdflib.o src/split.o rm -f ssw_cpp.o ssw.o rm -f libvcflib.so rm -rf binaries rm -rf lib rm -rf include rm -rf obj # cd tabixpp && make clean # cd smithwaterman && make clean # cd fastahack && make clean make[1]: Leaving directory '/<>/libvcflib-1.0.0~rc1+dfsg1' dh_autoreconf_clean debian/rules override_dh_clean make[1]: Entering directory '/<>/libvcflib-1.0.0~rc1+dfsg1' dh_clean find . -name "*.o" -delete make[1]: Leaving directory '/<>/libvcflib-1.0.0~rc1+dfsg1' 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 '/<>/libvcflib-1.0.0~rc1+dfsg1' dh_auto_build make -j16 make[2]: Entering directory '/<>/libvcflib-1.0.0~rc1+dfsg1' make[2]: git: Command not found if [ ! -d binaries ]; then mkdir -p binaries; fi if [ ! -d lib ]; then mkdir -p lib; fi if [ ! -d include ]; then mkdir -p include; fi if [ ! -d obj ]; then mkdir -p obj; fi echo "Source does not contain dir multichoose" #mkdir -p filevercmp echo "Source does not contain dir intervaltree" Source does not contain dir multichoose # cd multichoose && make && cp *.h* /<>/libvcflib-1.0.0~rc1+dfsg1/include/ #cp /usr/share/gnulib/lib/filevercmp.* filevercmp Source does not contain dir intervaltree # cd intervaltree && make && cp *.h* /<>/libvcflib-1.0.0~rc1+dfsg1/include/ #echo 'Proper use of filevercmp would be: `gnulib-tool --import filevercmp` - but it needs ./configure.ac' mkdir -p /<>/libvcflib-1.0.0~rc1+dfsg1/include/ && cp -a debian/include/* /<>/libvcflib-1.0.0~rc1+dfsg1/include/ #We here go with quilt patches from upstream files cd filevercmp && g++ -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" -fPIC -c filevercmp.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated ln -sf ../filevercmp/filevercmp.h /<>/libvcflib-1.0.0~rc1+dfsg1/include/filevercmp.h g++ -c -g -O2 -fdebug-prefix-map=/<>/libvcflib-1.0.0~rc1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -o src/Variant.o src/Variant.cpp `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" && cp src/*.h* /<>/libvcflib-1.0.0~rc1+dfsg1/include/ g++ -c -g -O2 -fdebug-prefix-map=/<>/libvcflib-1.0.0~rc1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -o src/rnglib.o src/rnglib.cpp `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" && cp src/*.h* /<>/libvcflib-1.0.0~rc1+dfsg1/include/ g++ -c -g -O2 -fdebug-prefix-map=/<>/libvcflib-1.0.0~rc1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -o src/var.o src/var.cpp `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" && cp src/*.h* /<>/libvcflib-1.0.0~rc1+dfsg1/include/ g++ -c -g -O2 -fdebug-prefix-map=/<>/libvcflib-1.0.0~rc1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -o src/pdflib.o src/pdflib.cpp `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" && cp src/*.h* /<>/libvcflib-1.0.0~rc1+dfsg1/include/ g++ -c -g -O2 -fdebug-prefix-map=/<>/libvcflib-1.0.0~rc1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -o src/cdflib.o src/cdflib.cpp `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" && cp src/*.h* /<>/libvcflib-1.0.0~rc1+dfsg1/include/ g++ -c -g -O2 -fdebug-prefix-map=/<>/libvcflib-1.0.0~rc1+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -o src/split.o src/split.cpp `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" && cp src/*.h* /<>/libvcflib-1.0.0~rc1+dfsg1/include/ clangclang: : warning: -Wl,-z,relro: 'linker' input unused warning: -Wl,-z,relro: 'linker' input unusedclang : warning: -Wl,-z,now: 'linker' input unused clang: clangwarning: : warning-lvcflib: 'linker' input unused: -Wl,-z,now: 'linker' input unused clang: warning: clang-lhts: 'linker' input unused: warning: -lvcflib: 'linker' input unused clang: warning: clang-lpthread: 'linker' input unusedclang: warning: : -lhts: 'linker' input unused clang: warning: -lz: 'linker' input unused clang: warningwarning: clang: -Wl,-z,relro: 'linker' input unused: -lpthread: 'linker' input unused warning : -lm: 'linker' input unused clang: warningclangclang: : -lz: 'linker' input unused: warning warning: : -Wl,-z,now: 'linker' input unused-ltabixpp: 'linker' input unused clang : warning: -lm: 'linker' input unused clangclang: : clangwarningwarning: : : -lsmithwaterman: 'linker' input unused-lvcflib: 'linker' input unused warning: -ltabixpp: 'linker' input unused clang: clangclangwarning: : : warningwarning-ldisorder: 'linker' input unused: : -lsmithwaterman: 'linker' input unused-lhts: 'linker' input unused clang: warning: clang-lfastahack: 'linker' input unusedclangclang: : : warningwarning: clang: -ldisorder: 'linker' input unused-lpthread: 'linker' input unused: warningwarning: clang: -Wl,-z,relro: 'linker' input unused: clangwarning-ldisorder: 'linker' input unused : : warning-lfastahack: 'linker' input unused: -lz: 'linker' input unused clang: clangwarning: clang: warningclang: -Wl,-z,now: 'linker' input unused: warning: -ldisorder: 'linker' input unused: -lm: 'linker' input unused clang: warning: clangwarning: -lvcflib: 'linker' input unusedwarning : : -ltabixpp: 'linker' input unused -Wl,-z,relro: 'linker' input unusedclang : clangwarning: : warning-lhts: 'linker' input unused: clang-lsmithwaterman: 'linker' input unused : warning: -Wl,-z,now: 'linker' input unused clangclang: : warningwarning: clang: -lpthread: 'linker' input unused: -ldisorder: 'linker' input unusedwarning : -lvcflib: 'linker' input unused clangclang: : warningwarningclang: : : -lz: 'linker' input unusedwarning -lfastahack: 'linker' input unused: -lhts: 'linker' input unused clang: warning: clang-lm: 'linker' input unused: clangwarning : : warning-ldisorder: 'linker' input unused: clang-lpthread: 'linker' input unused: warning: -ltabixpp: 'linker' input unusedclang : warning: -lz: 'linker' input unused clang: warning: -lsmithwaterman: 'linker' input unusedclang : warning: -lm: 'linker' input unused clang: warning: clang-ldisorder: 'linker' input unused: warning: -ltabixpp: 'linker' input unused clang: warning: clang-lfastahack: 'linker' input unused: warning: -lsmithwaterman: 'linker' input unused clang: warning: clang-ldisorder: 'linker' input unused: warning: -ldisorder: 'linker' input unused clang: warning: -lfastahack: 'linker' input unused clang: warning: -ldisorder: 'linker' input unused clang: warning: -Wl,-z,relro: 'linker' input unused clang: warning: -Wl,-z,now: 'linker' input unused clang: warning: -lvcflib: 'linker' input unused clang: warning: -lhts: 'linker' input unused clang: warning: -lpthread: 'linker' input unused clang: warning: -lz: 'linker' input unused clang: warning: -lm: 'linker' input unused clang: warning: -ltabixpp: 'linker' input unused clang: warning: -lsmithwaterman: 'linker' input unused clang: warning: -ldisorder: 'linker' input unused clang: warning: -lfastahack: 'linker' input unused clang: warning: -ldisorder: 'linker' input unused clangclang: : warningwarning: : argument unused during compilation: '-Llib'argument unused during compilation: '-Llib' clang: warning: argument unused during compilation: '-Llib' clangclang: : warningwarning: : argument unused during compilation: '-Llib' argument unused during compilation: '-Llib' clang: warning: argument unused during compilation: '-Llib' src/cdflib.cpp:2223:36: warning: '&&' within '||' [-Wlogical-op-parentheses] if(!(*s < 0.0e0 || *which != 3 && *s > *xn)) goto S160; ~~ ~~~~~~~~~~~~^~~~~~~~~~~ src/cdflib.cpp:2223:36: note: place parentheses around the '&&' expression to silence this warning if(!(*s < 0.0e0 || *which != 3 && *s > *xn)) goto S160; ^ ( ) src/cdflib.cpp:3909:20: warning: '&&' within '||' [-Wlogical-op-parentheses] if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; ~~~~~~^~~~~~~~~~~~~~ ~~ src/cdflib.cpp:3909:20: note: place parentheses around the '&&' expression to silence this warning if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; ^ ( ) src/cdflib.cpp:3909:45: warning: '&&' within '||' [-Wlogical-op-parentheses] if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; ~~ ~~~~~~~^~~~~~~~~~~~~~~ src/cdflib.cpp:3909:45: note: place parentheses around the '&&' expression to silence this warning if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; ^ ( ) src/cdflib.cpp:6924:17: warning: '&&' within '||' [-Wlogical-op-parentheses] qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; ~~~~~~^~~~~~~~~~~~~ ~~ src/cdflib.cpp:6924:17: note: place parentheses around the '&&' expression to silence this warning qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; ^ ( ) src/cdflib.cpp:6924:41: warning: '&&' within '||' [-Wlogical-op-parentheses] qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; ~~ ~~~~~~~^~~~~~~~~~~~~ src/cdflib.cpp:6924:41: note: place parentheses around the '&&' expression to silence this warning qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; ^ ( ) src/cdflib.cpp:6946:18: warning: '&&' within '||' [-Wlogical-op-parentheses] qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; ~~~~~~^~~~~~~~~~~~~~ ~~ src/cdflib.cpp:6946:18: note: place parentheses around the '&&' expression to silence this warning qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; ^ ( ) src/cdflib.cpp:6946:43: warning: '&&' within '||' [-Wlogical-op-parentheses] qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; ~~ ~~~~~~~^~~~~~~~~~~~~~ src/cdflib.cpp:6946:43: note: place parentheses around the '&&' expression to silence this warning qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; ^ ( ) src/cdflib.cpp:6985:18: warning: '&&' within '||' [-Wlogical-op-parentheses] qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; ~~~~~~^~~~~~~~~~~~~~ ~~ src/cdflib.cpp:6985:18: note: place parentheses around the '&&' expression to silence this warning qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; ^ ( ) src/cdflib.cpp:6985:43: warning: '&&' within '||' [-Wlogical-op-parentheses] qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; ~~ ~~~~~~~^~~~~~~~~~~~~~ src/cdflib.cpp:6985:43: note: place parentheses around the '&&' expression to silence this warning qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; ^ ( ) src/cdflib.cpp:7190:26: warning: '&&' within '||' [-Wlogical-op-parentheses] qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; ~~~~~~~~~~~~^~~~~~~~~~~~~~ ~~ src/cdflib.cpp:7190:26: note: place parentheses around the '&&' expression to silence this warning qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; ^ ( ) src/cdflib.cpp:7190:55: warning: '&&' within '||' [-Wlogical-op-parentheses] qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; ~~ ~~~~~~~~~~~^~~~~~~~~~~~~~ src/cdflib.cpp:7190:55: note: place parentheses around the '&&' expression to silence this warning qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; ^ ( ) src/Variant.cpp:225:5: warning: control may reach end of non-void function [-Wreturn-type] } ^ src/Variant.cpp:347:5: warning: control may reach end of non-void function [-Wreturn-type] } ^ src/Variant.cpp:381:5: warning: control may reach end of non-void function [-Wreturn-type] } ^ src/Variant.cpp:419:5: warning: control may reach end of non-void function [-Wreturn-type] } ^ 11 warnings generated. 4 warnings generated. # ar rs libvcflib.a src/Variant.o src/rnglib.o src/var.o src/pdflib.o src/cdflib.o src/split.o filevercmp/filevercmp.o gcc -shared -Wl,-soname -Wl,libvcflib.so.1 -o libvcflib.so.1 src/Variant.o src/rnglib.o src/var.o src/pdflib.o src/cdflib.o src/split.o filevercmp/filevercmp.o ln -s libvcflib.so.1 libvcflib.so cp -a libvcflib.so* lib g++ src/vcfecho.cpp -o binaries/vcfecho `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" g++ src/dumpContigsFromHeader.cpp -o binaries/dumpContigsFromHeader `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" g++ src/bFst.cpp -o binaries/bFst `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" g++ src/hapLrt.cpp -o binaries/hapLrt `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" g++ src/popStats.cpp -o binaries/popStats `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" g++ src/wcFst.cpp -o binaries/wcFst `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" g++ src/iHS.cpp -o binaries/iHS `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" g++ src/segmentFst.cpp -o binaries/segmentFst `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" g++ src/segmentIhs.cpp -o binaries/segmentIhs `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" g++ src/genotypeSummary.cpp -o binaries/genotypeSummary `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" g++ src/sequenceDiversity.cpp -o binaries/sequenceDiversity `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" g++ src/pFst.cpp -o binaries/pFst `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" g++ src/smoother.cpp -o binaries/smoother `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" g++ src/LD.cpp -o binaries/LD `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" g++ src/plotHaps.cpp -o binaries/plotHaps `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" g++ src/abba-baba.cpp -o binaries/abba-baba `pkg-config --cflags libsmithwaterman` `pkg-config --cflags libfastahack` -Iinclude -Wl,-z,relro -Wl,-z,now -Llib -lvcflib -lhts -lpthread -lz -lm -fopenmp -ltabixpp `pkg-config --libs libsmithwaterman` `pkg-config --libs libfastahack` -ldisorder -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"\" src/iHS.cpp:17:10: fatal error: 'omp.h' file not found #include ^ 1 error generated. Makefile:177: recipe for target 'binaries/iHS' failed make[2]: *** [binaries/iHS] Error 1 make[2]: *** Waiting for unfinished jobs.... src/sequenceDiversity.cpp:282:16: warning: equality comparison result unused [-Wunused-comparison] derived == 1; ~~~~~~~~^~~~ src/sequenceDiversity.cpp:282:16: src/abba-baba.cppnote: use '=' to turn this equality comparison into an assignment derived == 1; ^~ = :74:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ src/LD.cpp:253:16: warning: equality comparison result unused [-Wunused-comparison] derived == 1; ~~~~~~~~^~~~ src/LD.cpp:253:16: note: use '=' to turn this equality comparison into an assignment derived == 1; ^~ = /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:177: recipe for target 'binaries/segmentIhs' failed make[2]: *** [binaries/segmentIhs] Error 1 /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:177: recipe for target 'binaries/segmentFst' failed make[2]: *** [binaries/segmentFst] Error 1 /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:177: recipe for target 'binaries/vcfecho' failed make[2]: *** [binaries/vcfecho] Error 1 /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:177: recipe for target 'binaries/dumpContigsFromHeader' failed make[2]: *** [binaries/dumpContigsFromHeader] Error 1 /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:177: recipe for target 'binaries/smoother' failed make[2]: *** [binaries/smoother] Error 1 1 warning generated. /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:177: recipe for target 'binaries/abba-baba' failed make[2]: *** [binaries/abba-baba] Error 1 /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:177: recipe for target 'binaries/wcFst' failed make[2]: *** [binaries/wcFst] Error 1 /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:177: recipe for target 'binaries/genotypeSummary' failed make[2]: *** [binaries/genotypeSummary] Error 1 /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:177: recipe for target 'binaries/plotHaps' failed make[2]: *** [binaries/plotHaps] Error 1 /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:177: recipe for target 'binaries/pFst' failed make[2]: *** [binaries/pFst] Error 1 /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:177: recipe for target 'binaries/popStats' failed make[2]: *** [binaries/popStats] Error 1 1 warning generated. 1 warning generated. /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:177: recipe for target 'binaries/sequenceDiversity' failed make[2]: *** [binaries/sequenceDiversity] Error 1 /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:177: recipe for target 'binaries/LD' failed make[2]: *** [binaries/LD] Error 1 /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:177: recipe for target 'binaries/hapLrt' failed make[2]: *** [binaries/hapLrt] Error 1 /usr/bin/ld: cannot find -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) Makefile:177: recipe for target 'binaries/bFst' failed make[2]: *** [binaries/bFst] Error 1 make[2]: Leaving directory '/<>/libvcflib-1.0.0~rc1+dfsg1' dh_auto_build: make -j16 returned exit code 2 debian/rules:15: recipe for target 'override_dh_auto_build' failed make[1]: *** [override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>/libvcflib-1.0.0~rc1+dfsg1' debian/rules:8: 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 2017-07-06T15:48:56Z 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: 61640 Build-Time: 11 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 8 Job: libvcflib_1.0.0~rc1+dfsg1-5 Machine Architecture: amd64 Package: libvcflib Package-Time: 41 Source-Version: 1.0.0~rc1+dfsg1-5 Space: 61640 Status: attempted Version: 1.0.0~rc1+dfsg1-5 -------------------------------------------------------------------------------- Finished at 2017-07-06T15:48:56Z Build needed 00:00:41, 61640k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 41.231433478s DC-Time-Estimation: 41.231433478 versus expected 1 (r/m: 40.231433478 ; m: 1.0)